https://wiki.yeastgenome.org/api.php?action=feedcontributions&user=Kmacpher&feedformat=atomSGD-Wiki - User contributions [en]2024-03-29T12:01:27ZUser contributionsMediaWiki 1.31.14https://wiki.yeastgenome.org/index.php?title=File:alliance_brochure.pdf&diff=401169File:alliance brochure.pdf2019-08-15T21:09:28Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter_Archives&diff=401125SGD Newsletter Archives2019-06-03T16:53:17Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
SGD periodically publishes a community newsletters. This page contains links to the SGD Newsletters that have been released, listed in chronological order. Click on a date to see the newsletter published on that date.<br />
<br />
{| width="50%" border="1" <br />
| '''2019'''<br />
|<br />
|[[SGD_Newsletter,_Spring_2019 | 2019-05-29]] <br />
|<br />
|<br />
|-<br />
|'''2018'''<br />
| <br />
|[[SGD_Newsletter,_April_2018 | 2018-04-30]]<br />
|[[SGD_Newsletter,_Fall_2018 | 2018-10-05]] <br />
|<br />
|-bgcolor="E6E6FA"<br />
|'''2017'''<br />
| <br />
|<br />
| <br />
| [[SGD_Newsletter,_December_2017 | 2017-12-20]]<br />
|-<br />
|'''2016'''<br />
| [[SGD_Newsletter,_March_2016 | 2016-03-14]]<br />
|<br />
| [[SGD_Newsletter,_August_2016|2016-08-29]]<br />
| [[SGD_Newsletter,_December_2016 | 2016-12-20]]<br />
|- bgcolor="E6E6FA"<br />
| '''2015'''<br />
| [[SGD_Quarterly_Newsletter,_Spring_2015| 2015-02-26]]<br />
|<br />
| [[SGD_Quarterly_Newsletter,_Summer_2015 | 2015-08-28]]<br />
| [[SGD_Newsletter,_December_2015 | 2015-12-18]]<br />
|-<br />
| '''2014'''<br />
|<br />
| [[SGD_Quarterly_Newsletter,_Spring_2014| 2014-04-17]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2014| 2014-07-23]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2014|2014-10-15]]<br />
|- bgcolor="E6E6FA"<br />
| '''2013'''<br />
|<br />
| [[SGD_Quarterly_Newsletter,_Summer_2013| 2013-06-10]]<br />
|<br />
| [[SGD_Quarterly_Newsletter,_Winter_2013| 2013-12-16]]<br />
|-<br />
| '''2012'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2012| 2012-01-27]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2012| 2012-04-28]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2012| 2012-08-22]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2012| 2012-12-13]]<br />
|- bgcolor="E6E6FA"<br />
| '''2011'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2011| 2011-02-18]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2011| 2011-05-05]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2011| 2011-08-11]]<br />
| <br />
|-<br />
| '''2010'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2010| 2010-01-29]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2010| 2010-04-29]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2010| 2010-07-22]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2010| 2010-11-01]]<br />
|- bgcolor="E6E6FA"<br />
| '''2009'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2009| 2009-02-03]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2009| 2009-05-01]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2009| 2009-08-04]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2009| 2009-11-06]]<br />
|-<br />
| '''2008'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2008| 2008-01-31]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2008| 2008-04-30]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2008| 2008-07-31]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2008| 2008-11-03]]<br />
|- bgcolor="E6E6FA"<br />
| '''2007'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2007| 2007-01-29]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2007| 2007-05-07]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2007| 2007-07-30]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2007| 2007-11-08]]<br />
|-<br />
| '''2006'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2006| 2006-02-02]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2006| 2006-05-01]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2006| 2006-07-20]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2006| 2006-11-01]]<br />
|- bgcolor="E6E6FA"<br />
| '''2005'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2005| 2005-01-31]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2005| 2005-04-28]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2005| 2005-07-29]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2005| 2005-10-24]]<br />
|-<br />
| '''2004'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2004| 2004-01-30]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2004| 2004-04-26]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2004| 2004-07-23]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2004| 2004-11-18]]<br />
|- bgcolor="E6E6FA"<br />
| '''2003'''<br />
| [[SGD_Quarterly_Newsletter,_Winter_2003| 2003-01-31]]<br />
| [[SGD_Quarterly_Newsletter,_Spring_2003| 2003-04-28]]<br />
| [[SGD_Quarterly_Newsletter,_Summer_2003| 2003-08-04]]<br />
| [[SGD_Quarterly_Newsletter,_Fall_2003| 2003-10-31]]<br />
|-<br />
|}</div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=Meetings&diff=400363Meetings2019-02-08T20:44:17Z<p>Kmacpher: /* Upcoming Conferences & Courses */</p>
<hr />
<div>Meetings that may be of interest to the yeast community are listed below. If you would like to add a conference or meeting to the list, please log in to the wiki. If you do not have a user account, please contact the [http://www.yeastgenome.org/cgi-bin/suggestion SGD helpdesk] and we will gladly create an account for you.<br />
<br />
=Upcoming Conferences & Courses =<br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2019 Fungal Pathogen Genomics]</b><br><br />
Wellcome Genome Campus, Hinxton, Cambridge, UK<br><br />
May 7 - 12, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC2019]</b><br><br />
Ljubljana, Slovenia <br><br />
May 22 - 24, 2019<br><br />
<br />
<b>[http://www.efbiotechnology.org/PYFF/ 7th Conference on Physiology of Yeasts & Filamentous Fungi (PYFF)]</b><br><br />
Milan, Italy<br><br />
June 24 to June 27, 2019<br><br />
<br />
<b>[https://ssbss2019.icas.xyz 6th International Synthetic & Systems Biology Summer School - SSBSS 2019]</b><br><br />
Scuola Normale Superiore di Pisa, Tuscany, Italy<br><br />
July 22 - 26, 2019<br><br />
<br />
<b>[https://meetings.cshl.edu/courses.aspx?course=C-yeas&year=19 CSHL Yeast Genetics & Genomics course]</b><br><br />
Cold Spring Harbor, NY<br><br />
July 23 - August 12, 2019<br><br />
<br />
<b>[https://yeast2019.org/ 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)]</b><br><br />
Gothenburg, Sweden<br><br />
August 18 - 22, 2019<br><br />
<br />
<b>[http://www.issy35.com/en/index.html 35th International Specialised Symposium on Yeasts (ISSY)]</b><br><br />
Antalya, Turkey<br><br />
October 21 - 25, 2019<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/tagc/2020/index The Allied Genetics Conference - TAGC 2020]</b><br><br />
Metro Washington, DC <br><br />
April 22 - 26, 2020<br><br />
<br />
=Past Yeast Meetings=<br />
<br />
<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com/ 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, New South Wales, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<br />
<b>International Conference on Yeast Genetics and Molecular Biology</b><BR><br />
:Browse or search abstracts:<BR><br />
:[http://onlinelibrary.wiley.com/doi/10.1002/yea.v32.s1/issuetoc 2015] (XXVII) | [http://onlinelibrary.wiley.com/doi/10.1002/yea.v30.S1/issuetoc 2013] (XXVI) | [http://onlinelibrary.wiley.com/doi/10.1002/yea.1862/abstract 2011] (XXV) | [http://onlinelibrary.wiley.com/doi/10.1002/yea.1682/abstract 2009] (XXIV) <br />
<br />
<b>Yeast Genetics & Molecular Biology Meeting</b><BR><br />
:Browse or search abstracts; view participant lists and photos:<BR><br />
:[http://wiki.yeastgenome.org/index.php/File:Program_Book_Abstracts_Yeast_2014.pdf 2014 (PDF abstract book)] | [http://www.yeast-meet.org/2012/ 2012] | [http://www.yeast-meet.org/2010/ 2010] | [http://www.yeast-meet.org/2008 2008]</div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=Positions_in_yeast_labs&diff=400346Positions in yeast labs2018-12-07T22:58:33Z<p>Kmacpher: </p>
<hr />
<div>=='''Systems Chemical Biologist at Yumanity Therapeutics (posted 7 December 2018)'''==<br />
'''Description:''' Yumanity Therapeutics (http://www.yumanity.com/) is transforming drug discovery for neurodegenerative diseases caused by protein misfolding. Even though an estimated 50 million people worldwide suffer from diseases affecting the brain and central nervous system, there are no approved disease-modifying therapies or cures. Yumanity is working to identify and develop new, disease-modifying therapies that address illnesses such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS). The company’s approach concentrates on correcting the cellular pathologies driven by misfolded proteins, the altered biology or phenotypes driving these diseases.<br />
<br />
'''Position Overview:'''<br />
The systems chemical biologist will work as an integral part of the target identification team, which uses large-scale forward and reverse genetic approaches to reveal the cellular targets of compounds discovered from phenotypic screens. The position reports to the target identification team lead, and will interact across all Yumanity’s core platforms, including chemistry, yeast screening, and mammalian validation. The successful candidate will become a key individual contributor in a dynamic and multidisciplinary environment. They will demonstrate a respect for others and be highly effective in a team.<br />
<br />
For more information on this position, please visit the Yumanity careers page (http://www.yumanity.com/careers/). If you would like to apply, please submit your CV with the "Systems Chemical Biologist" in the subject line to [mailto:careers@yumanity.com careers@yumanity.com].<br />
<br />
=='''Postdoctoral Researcher or Research Scientist Position (1 position) in the Boone Team (RIKEN, Japan) (posted 7 December 2018)'''==<br />
A Postdoctoral Researcher or Research Scientist position is available in Dr. Charles Boone’s laboratory at RIKEN (http://www.riken.jp/en/research/labs/csrs/mol_ligand_targ). We are seeking a highly motivated candidate with strong expertise in yeast genetics/molecular biology and human cell culture experiments. The candidate will develop innovative techniques based on genetic networks in yeast and human cells that leads to quick and accurate detection of the ligand-target interactions. <br />
<br />
'''How to apply:''' Please check the website (http://www.riken.jp/en/careers/researchers/20181129_5/) for the details.<br />
<br />
=='''Postdoctoral Position in Yeast Molecular Biology (posted 5 September 2018)'''==<br />
A NIH-funded postdoctoral position is available in the laboratory of Dr. David Kadosh in the Department of Microbiology, Immunology & Molecular Genetics at the University of Texas Health Science Center at San Antonio. Research will use cutting-edge techniques to study molecular mechanisms that control gene expression, morphology, virulence and virulence-related properties in response to host environmental cues in the yeast ''Candida albicans'', a major human fungal pathogen. For additional details and previous publications, please see https://wp.uthscsa.edu/mimg/team-member/david-kadosh-ph-d/. <br />
<br><br><br />
Highly motivated individuals with previous experience and a strong track record in molecular biology, genomics, cell biology, genetics, bioinformatics and/or protein chemistry are especially encouraged to apply. Previous experience in fungal pathogenesis is not necessarily required. Please send a cover letter outlining your research interests, CV, and contact information for three references to David Kadosh (kadosh@uthscsa.edu). <br />
<br><br><br />
Many opportunities are available for collaboration with both basic and clinical researchers at the large and internationally recognized San Antonio Center for Medical Mycology (see http://www.sacmm.org/). <br />
<br><br><br />
The successful applicant will receive equivalent to NIH-level salary and full benefits. Located in south central Texas, near both Austin and the Texas Hill Country, San Antonio is one of the lowest cost-of-living major metropolitan areas in the U.S. <br />
<br><br><br />
All postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Employment Opportunity/Affirmative Action Employer. <br />
<br />
<br />
=='''The Kupiec lab is recruiting PhD students and post-docs (posted 2 July 2018)'''==<br />
'''Description''': PhD positions and post-doctoral research positions are available in Prof. Martin Kupiec’s laboratory at Tel Aviv University (https://mkyeastlab.wixsite.com/mklab). We work with yeast (''S. cerevisiae'' and ''S. pombe'') exploring the role of Elg1 and other proteins in genome stability maintenance and telomere biology. Additional projects include exploring the interphase between DNA replication, chromatin modifications, sister-chromatid cohesion and DNA repair.<br />
<br><br><br />
We are seeking highly motivated candidates with expertise in molecular biology and genetics. Experience in yeast genetics is desirable, but not a requirement. Independence, communication and interpersonal skills are valued in order to work in a young, dynamic, diverse, and collaborative environment. We are an international team, and research is carried out in English.<br />
<br><br><br />
'''How to apply''': Prospective candidates should submit a '''cover letter''' describing their research experience, scientific interest, career goals, and motivation to apply for this position. Please include an '''updated CV''' and the contact information of '''at least two references'''. Questions should be directed to Prof. Martin Kupiec at martin@post.tau.ac.il.<br />
<br />
=='''Synthetic Molecular Biologist (posted 17 January 2018)'''==<br />
Gadusol Laboratories, a new biotech startup, has an '''immediate opening''' for a qualified and motivated full-time Synthetic Molecular Biologist at our Corvallis, Oregon laboratory. <br />
<br />
Job Description: <br><br />
Manage a 12-month National Science Foundation SBIR Phase I research effort to produce marine-based sunscreens in yeast. <br />
The position includes executing a scope of work focused on attaining high yields of recombinant sunscreen compounds in yeast and entails all aspects of research management, including but not limited to: fulfilling all grant requirements of a Principal Investigator, reporting, laboratory maintenance, and performing various operational and administrative activities as needed. The candidate we seek is comfortable working independently, adapts well to change, is willing to work closely with senior management to help secure follow-on funding (i.e., contribute to SBIR Phase 2 proposal development), and enjoys working in fast-paced startup environment with room for growth. <br />
<br />
The position requires some travel. <br />
<br />
Requirements:<br />
* Ph.D. in Microbiology, Biology, Genetics, or Biochemistry <br />
* Experience with yeast molecular genetics preferred <br />
* Interest in working for a startup and participating in strategic growth <br />
* Travel to a key conference occurring March 18 – 21, 2018 <br />
<br />
Salary: Commensurate with experience. <br />
<br />
Please send a resume and cover letter to info@gadusollabs.com for consideration.<br />
<br />
=='''Postdoc Position in Ubiquitination and Stress Response at Duke University (posted 08 November 2017)'''==<br />
<br />
'''Description:''' A post-doctoral research position is available in Dr. Gustavo Silva’s laboratory at Duke University (https://sites.duke.edu/silvalab). The prospective candidate will develop research focused on understanding the role of protein ubiquitination and protein dynamics during cellular response to stress. The lab uses a combination of molecular and large scale approaches, including mass spectrometry-based proteomics and next generation sequencing, to elucidate signaling pathways in yeast and mammalian cells.<br />
<br />
<br />
'''Candidate:''' We are seeking a highly motivated candidate with strong expertise in molecular cloning, recombinant protein, and yeast genetics to fulfill this position. Additional experience in proteomics, genomics, and/or computational biology will be favored and is desirable, but not a requirement. Communication and interpersonal skills are valued in order to work in a young, dynamic, diverse, and collaborative environment<br />
<br />
<br />
'''How to apply:'''Prospective candidates should submit a '''cover letter''' describing their research experience, scientific interest, career goals, and motivation to apply for this position. Please include an '''updated CV''' and the contact information of '''three references'''. Questions should be directed to Dr. Silva at gustavo.silva@duke.edu and applications must be submitted via Academic Jobs Online: '''https://academicjobsonline.org/ajo/jobs/10359'''<br />
<br />
<br />
=='''Postdoc Opening - Autophagy of lipid droplets in YEAST (posted 29 August 2017)'''==<br />
<br />
'''Postdoctoral project:''' Autophagy of lipid droplets in YEAST<br />
<br />
::'''Academic institution:''' University of California, San Diego<br />
::<br />
::'''Academic division:''' Division of Biological Sciences<br />
::<br />
::'''Academic unit:''' Section of Molecular Biology<br />
<br />
'''Description:''' Applications are invited for a postdoctoral position in the group of Taras Nazarko studying mechanisms of lipophagy, the selective autophagy of lipid droplets (LDs). Lipophagy is accomplished by delivery of LDs from the cytosol to the lysosome (or vacuole in yeast). As in other autophagic pathways, the core autophagic machinery forms the autophagic isolation membrane that sequesters the LD from the cytosol. However, how this autophagic membrane recognizes the LD after lipophagy induction is unknown. Also, it is not clear how lipophagy is kept in check the rest of the time. Therefore, lipophagy selectivity and regulation are the key gaps in our understanding of this pathway. A postdoctoral scholar will develop a project in one of these areas. Mechanistic understanding in these areas is critical for the precise control of lipophagy in humans for the prevention and treatment of various lipid accumulation diseases, like atherosclerosis and obesity. Initial appointment is for 1 year with possible extension for up to 5 years of overall postdoctoral training. Salary is commensurate with experience (http://postdoc.ucsd.edu/appointment-guidelines/).<br />
<br />
'''Applicant requirements:''' The successful applicants will have a recent PhD in biochemistry, genetics, molecular or cell biology and a strong background in YEAST genetics, protein biochemistry and fluorescence microscopy. Expertise with mammalian cells or zebrafish model is a plus but not essential. Preference will be given to candidates with experience in autophagy pathway or with LDs.<br />
<br />
'''How to apply:''' Please send your cover letter, CV and contact information of 3 references to Taras Nazarko, tnazarko@ucsd.edu</div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=Positions_in_yeast_labs&diff=400345Positions in yeast labs2018-12-07T17:20:02Z<p>Kmacpher: </p>
<hr />
<div>=='''Postdoctoral Researcher or Research Scientist Position (1 position) in the Boone Team (RIKEN, Japan) (posted 7 December 2018)'''==<br />
A Postdoctoral Researcher or Research Scientist position is available in Dr. Charles Boone’s laboratory at RIKEN (http://www.riken.jp/en/research/labs/csrs/mol_ligand_targ). We are seeking a highly motivated candidate with strong expertise in yeast genetics/molecular biology and human cell culture experiments. The candidate will develop innovative techniques based on genetic networks in yeast and human cells that leads to quick and accurate detection of the ligand-target interactions. <br />
<br />
'''How to apply:''' Please check the website (http://www.riken.jp/en/careers/researchers/20181129_5/) for the details.<br />
<br />
=='''Postdoctoral Position in Yeast Molecular Biology (posted 5 September 2018)'''==<br />
A NIH-funded postdoctoral position is available in the laboratory of Dr. David Kadosh in the Department of Microbiology, Immunology & Molecular Genetics at the University of Texas Health Science Center at San Antonio. Research will use cutting-edge techniques to study molecular mechanisms that control gene expression, morphology, virulence and virulence-related properties in response to host environmental cues in the yeast ''Candida albicans'', a major human fungal pathogen. For additional details and previous publications, please see https://wp.uthscsa.edu/mimg/team-member/david-kadosh-ph-d/. <br />
<br><br><br />
Highly motivated individuals with previous experience and a strong track record in molecular biology, genomics, cell biology, genetics, bioinformatics and/or protein chemistry are especially encouraged to apply. Previous experience in fungal pathogenesis is not necessarily required. Please send a cover letter outlining your research interests, CV, and contact information for three references to David Kadosh (kadosh@uthscsa.edu). <br />
<br><br><br />
Many opportunities are available for collaboration with both basic and clinical researchers at the large and internationally recognized San Antonio Center for Medical Mycology (see http://www.sacmm.org/). <br />
<br><br><br />
The successful applicant will receive equivalent to NIH-level salary and full benefits. Located in south central Texas, near both Austin and the Texas Hill Country, San Antonio is one of the lowest cost-of-living major metropolitan areas in the U.S. <br />
<br><br><br />
All postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Employment Opportunity/Affirmative Action Employer. <br />
<br />
<br />
=='''The Kupiec lab is recruiting PhD students and post-docs (posted 2 July 2018)'''==<br />
'''Description''': PhD positions and post-doctoral research positions are available in Prof. Martin Kupiec’s laboratory at Tel Aviv University (https://mkyeastlab.wixsite.com/mklab). We work with yeast (''S. cerevisiae'' and ''S. pombe'') exploring the role of Elg1 and other proteins in genome stability maintenance and telomere biology. Additional projects include exploring the interphase between DNA replication, chromatin modifications, sister-chromatid cohesion and DNA repair.<br />
<br><br><br />
We are seeking highly motivated candidates with expertise in molecular biology and genetics. Experience in yeast genetics is desirable, but not a requirement. Independence, communication and interpersonal skills are valued in order to work in a young, dynamic, diverse, and collaborative environment. We are an international team, and research is carried out in English.<br />
<br><br><br />
'''How to apply''': Prospective candidates should submit a '''cover letter''' describing their research experience, scientific interest, career goals, and motivation to apply for this position. Please include an '''updated CV''' and the contact information of '''at least two references'''. Questions should be directed to Prof. Martin Kupiec at martin@post.tau.ac.il.<br />
<br />
=='''Synthetic Molecular Biologist (posted 17 January 2018)'''==<br />
Gadusol Laboratories, a new biotech startup, has an '''immediate opening''' for a qualified and motivated full-time Synthetic Molecular Biologist at our Corvallis, Oregon laboratory. <br />
<br />
Job Description: <br><br />
Manage a 12-month National Science Foundation SBIR Phase I research effort to produce marine-based sunscreens in yeast. <br />
The position includes executing a scope of work focused on attaining high yields of recombinant sunscreen compounds in yeast and entails all aspects of research management, including but not limited to: fulfilling all grant requirements of a Principal Investigator, reporting, laboratory maintenance, and performing various operational and administrative activities as needed. The candidate we seek is comfortable working independently, adapts well to change, is willing to work closely with senior management to help secure follow-on funding (i.e., contribute to SBIR Phase 2 proposal development), and enjoys working in fast-paced startup environment with room for growth. <br />
<br />
The position requires some travel. <br />
<br />
Requirements:<br />
* Ph.D. in Microbiology, Biology, Genetics, or Biochemistry <br />
* Experience with yeast molecular genetics preferred <br />
* Interest in working for a startup and participating in strategic growth <br />
* Travel to a key conference occurring March 18 – 21, 2018 <br />
<br />
Salary: Commensurate with experience. <br />
<br />
Please send a resume and cover letter to info@gadusollabs.com for consideration.<br />
<br />
=='''Postdoc Position in Ubiquitination and Stress Response at Duke University (posted 08 November 2017)'''==<br />
<br />
'''Description:''' A post-doctoral research position is available in Dr. Gustavo Silva’s laboratory at Duke University (https://sites.duke.edu/silvalab). The prospective candidate will develop research focused on understanding the role of protein ubiquitination and protein dynamics during cellular response to stress. The lab uses a combination of molecular and large scale approaches, including mass spectrometry-based proteomics and next generation sequencing, to elucidate signaling pathways in yeast and mammalian cells.<br />
<br />
<br />
'''Candidate:''' We are seeking a highly motivated candidate with strong expertise in molecular cloning, recombinant protein, and yeast genetics to fulfill this position. Additional experience in proteomics, genomics, and/or computational biology will be favored and is desirable, but not a requirement. Communication and interpersonal skills are valued in order to work in a young, dynamic, diverse, and collaborative environment<br />
<br />
<br />
'''How to apply:'''Prospective candidates should submit a '''cover letter''' describing their research experience, scientific interest, career goals, and motivation to apply for this position. Please include an '''updated CV''' and the contact information of '''three references'''. Questions should be directed to Dr. Silva at gustavo.silva@duke.edu and applications must be submitted via Academic Jobs Online: '''https://academicjobsonline.org/ajo/jobs/10359'''<br />
<br />
<br />
=='''Postdoc Opening - Autophagy of lipid droplets in YEAST (posted 29 August 2017)'''==<br />
<br />
'''Postdoctoral project:''' Autophagy of lipid droplets in YEAST<br />
<br />
::'''Academic institution:''' University of California, San Diego<br />
::<br />
::'''Academic division:''' Division of Biological Sciences<br />
::<br />
::'''Academic unit:''' Section of Molecular Biology<br />
<br />
'''Description:''' Applications are invited for a postdoctoral position in the group of Taras Nazarko studying mechanisms of lipophagy, the selective autophagy of lipid droplets (LDs). Lipophagy is accomplished by delivery of LDs from the cytosol to the lysosome (or vacuole in yeast). As in other autophagic pathways, the core autophagic machinery forms the autophagic isolation membrane that sequesters the LD from the cytosol. However, how this autophagic membrane recognizes the LD after lipophagy induction is unknown. Also, it is not clear how lipophagy is kept in check the rest of the time. Therefore, lipophagy selectivity and regulation are the key gaps in our understanding of this pathway. A postdoctoral scholar will develop a project in one of these areas. Mechanistic understanding in these areas is critical for the precise control of lipophagy in humans for the prevention and treatment of various lipid accumulation diseases, like atherosclerosis and obesity. Initial appointment is for 1 year with possible extension for up to 5 years of overall postdoctoral training. Salary is commensurate with experience (http://postdoc.ucsd.edu/appointment-guidelines/).<br />
<br />
'''Applicant requirements:''' The successful applicants will have a recent PhD in biochemistry, genetics, molecular or cell biology and a strong background in YEAST genetics, protein biochemistry and fluorescence microscopy. Expertise with mammalian cells or zebrafish model is a plus but not essential. Preference will be given to candidates with experience in autophagy pathway or with LDs.<br />
<br />
'''How to apply:''' Please send your cover letter, CV and contact information of 3 references to Taras Nazarko, tnazarko@ucsd.edu</div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400342SGD Newsletter, Fall 20182018-10-04T22:17:07Z<p>Kmacpher: /* 25th Anniversary of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiated in 1993 for Unix workstations and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Disease Ontology page for "cancer"]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|315px|right|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex]) provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
<br><br />
You may have seen SGD representatives at the following courses:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=19 Yeast Genetics and Genomics course] at [https://www.cshl.edu/ CSHL] in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the [https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2018/ Fungal Pathogen Genomics course] at the [https://www.wellcomegenomecampus.org Wellcome Genome Campus] in May. He taught students how to use tools and resources at both SGD and the [http://www.candidagenome.org/ ''Candida'' Genome Database].<br />
<br />
<br><br><br><br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/tagc/2020/index The Allied Genetics Conference (TAGC 2020)]</b><br><br />
Gaylord National Resort & Convention Center, Metro Washington, DC, UCA<br><br />
April 22 – 26, 2020<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400341SGD Newsletter, Fall 20182018-10-04T21:48:51Z<p>Kmacpher: /* Complex Pages Now Live */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Disease Ontology page for "cancer"]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|315px|right|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex]) provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
<br><br />
You may have seen SGD representatives at the following courses:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=19 Yeast Genetics and Genomics course] at [https://www.cshl.edu/ CSHL] in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the [https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2018/ Fungal Pathogen Genomics course] at the [https://www.wellcomegenomecampus.org Wellcome Genome Campus] in May. He taught students how to use tools and resources at both SGD and the [http://www.candidagenome.org/ ''Candida'' Genome Database].<br />
<br />
<br><br><br><br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/tagc/2020/index The Allied Genetics Conference (TAGC 2020)]</b><br><br />
Gaylord National Resort & Convention Center, Metro Washington, DC, UCA<br><br />
April 22 – 26, 2020<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400333SGD Newsletter, Fall 20182018-10-03T21:42:47Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Disease Ontology page for "cancer"]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|315px|right|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400332SGD Newsletter, Fall 20182018-10-03T21:39:36Z<p>Kmacpher: /* Complex Pages Now Live */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Disease Ontology page for "cancer"]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|right|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400331SGD Newsletter, Fall 20182018-10-03T21:38:30Z<p>Kmacpher: /* Disease Data Now Available */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Disease Ontology page for "cancer"]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400330SGD Newsletter, Fall 20182018-10-03T21:38:17Z<p>Kmacpher: /* Disease Data Now Available */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 Cancer Disease Ontology page]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400329SGD Newsletter, Fall 20182018-10-03T21:38:06Z<p>Kmacpher: /* Disease Data Now Available */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400328SGD Newsletter, Fall 20182018-10-03T21:37:24Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
Click on the image shown at the left for some quick examples, or view the entire collection at our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400327SGD Newsletter, Fall 20182018-10-03T21:35:36Z<p>Kmacpher: /* SGD API Examples */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|190px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400326SGD Newsletter, Fall 20182018-10-03T21:35:13Z<p>Kmacpher: /* SGD API Examples */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|left|350px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
<p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400325SGD Newsletter, Fall 20182018-10-03T21:34:02Z<p>Kmacpher: /* SGD API Examples */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|border|right|350px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400324SGD Newsletter, Fall 20182018-10-03T21:32:01Z<p>Kmacpher: /* SGD API Examples */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|thumb|right|350px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|Python examples for accessing SGD API]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? <br />
<br />
The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples.<br />
<br />
For some Python examples for accessing the SGD API, click on the image to the right.<br />
<br />
<p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</p><br />
<br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400323SGD Newsletter, Fall 20182018-10-03T21:29:00Z<p>Kmacpher: /* Disease Data Now Available */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|thumb|right|350px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|Python examples for accessing SGD API]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples<br />
<br />
<p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</p><br />
==Disease Data Now Available==<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|500px|link=https://www.yeastgenome.org/disease/DOID:162|thumb|center|The [https://www.yeastgenome.org/disease/DOID:162 cancer Disease Ontology page]]<br />
|[[File:ccc2_disease.gif|500px|thumb|center|caption|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400322SGD Newsletter, Fall 20182018-10-03T21:28:39Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|left|upright=.8|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br><br><br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
[[File:sgd-booth1.jpg|bottom|thumb|upright=.7|Staff members at the SGD booth]]<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
<br />
===Fun Stuff===<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<p>A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br><br></p><br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br><br><br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br><br />
<br />
==SGD API Examples==<br />
[[File:sgd-api-access-thumbnail2.jpg|thumb|right|350px|link=https://wiki.yeastgenome.org/images/5/53/sgd-api-access.jpg|Python examples for accessing SGD API]]<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found in our GitHub repository: https://github.com/yeastgenome/sgd_api_examples<br />
<br />
<p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</p><br />
==Disease Data Now Available==<br />
<br />
{| width="100%" <br />
|- style="vertical-align:middle;"<br />
|[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
|[[File:ccc2_disease.gif|thumb|600px|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
|}<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br />
==Complex Pages Now Live==<br />
<br />
[[File:complex_page.jpg|thumb|350px|left|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br>In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br><br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br><br><br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:cdc6-thumbnail.jpg&diff=400321File:cdc6-thumbnail.jpg2018-10-03T21:09:17Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:sgd-api-access-thumbnail2.jpg&diff=400310File:sgd-api-access-thumbnail2.jpg2018-10-03T20:41:49Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:sgd-api-access-thumbnail.jpg&diff=400309File:sgd-api-access-thumbnail.jpg2018-10-03T20:28:06Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400261SGD Newsletter, Fall 20182018-10-03T17:34:33Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400260SGD Newsletter, Fall 20182018-10-03T17:21:03Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018EngelSGDworkshop.pdf Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2e/Regulation2018poster.pdf Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:YGM2018EngelSGDworkshop.pdf&diff=400259File:YGM2018EngelSGDworkshop.pdf2018-10-03T17:20:52Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400258SGD Newsletter, Fall 20182018-10-03T17:04:52Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400257SGD Newsletter, Fall 20182018-10-03T17:03:28Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
<br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400256SGD Newsletter, Fall 20182018-10-03T16:56:22Z<p>Kmacpher: /* Upcoming Meetings */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[https://iysgc2018.com 7th International Yeast 2.0 and Synthetic Genomes Conference]</b><br><br />
Sydney, NSW, Australia<br><br />
November 26 - 28, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br><br />
<br />
<b>[http://www.ylc2019.alfa-faktor.si 14th Yeast Lipid Conference - YLC 2019]</b><br><br />
Ljubljana, Slovenia<br><br />
May 22 - 24, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400255SGD Newsletter, Fall 20182018-10-03T16:52:07Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Fall 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400253SGD Newsletter, Fall 20182018-10-03T16:51:52Z<p>Kmacpher: Kmacpher moved page SGD Newsletter, September 2018 to SGD Newsletter, Fall 2018</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_September_2018&diff=400254SGD Newsletter, September 20182018-10-03T16:51:52Z<p>Kmacpher: Kmacpher moved page SGD Newsletter, September 2018 to SGD Newsletter, Fall 2018</p>
<hr />
<div>#REDIRECT [[SGD Newsletter, Fall 2018]]</div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400252SGD Newsletter, Fall 20182018-10-03T16:50:57Z<p>Kmacpher: /* What else have we been up to lately? */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.8|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400251SGD Newsletter, Fall 20182018-10-03T16:50:50Z<p>Kmacpher: /* What else have we been up to lately? */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:wellcome_KM.jpg|thumb|left|upright=.9|Kevin MacPherson at the [https://www.wellcomegenomecampus.org/ Wellcome Genome Campus]]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:wellcome_KM.jpg&diff=400250File:wellcome KM.jpg2018-10-03T16:49:31Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400249SGD Newsletter, Fall 20182018-10-03T16:42:25Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400248SGD Newsletter, Fall 20182018-10-03T16:40:59Z<p>Kmacpher: /* Website Updates */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
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<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400247SGD Newsletter, Fall 20182018-10-03T16:40:31Z<p>Kmacpher: /* Variant Information in Sequence Tab */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
[[File:sequence-variants.png|thumb|right|upright=1.5|The [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence Variants section].]]<br />
On the Sequence summary tab for your favorite gene, we've added a new feature that lets you compare gene sequence variants between twelve commonly used ''S. cerevisiae'' strains. The Variants graph, derived from our [https://www.yeastgenome.org/variant-viewer Variant Viewer] tool, depicts all nucleotide or amino acid changes relative to strain S288C in an easy-to-read format. To find this information for your favorite gene, go to its gene summary page and click on the "Sequence" tab. The feature will be displayed in the Variants section (example: [https://www.yeastgenome.org/locus/S000004218/sequence#variants ECM22 Sequence summary tab])<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:sequence-variants.png&diff=400246File:sequence-variants.png2018-10-03T16:28:44Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400245SGD Newsletter, Fall 20182018-10-02T17:58:59Z<p>Kmacpher: /* Workshop: Getting More out of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_KM.pdf Tools and Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:YGM2018_workshop_KM.pdf&diff=400244File:YGM2018 workshop KM.pdf2018-10-02T17:57:51Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400243SGD Newsletter, Fall 20182018-10-02T17:51:35Z<p>Kmacpher: /* New and Improved Gene Sequence Resources */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as [https://www.yeastgenome.org/variant-viewer Variant Viewer]<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400242SGD Newsletter, Fall 20182018-10-02T17:50:33Z<p>Kmacpher: /* Complex Pages Now Live */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by running a search for the complex, or by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], simply [https://www.yeastgenome.org/search?q=GAL3-GAL80&category=complex run a search for "GAL3-GAL80"] and click on the Complexes category. Or, go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and locate the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400241SGD Newsletter, Fall 20182018-10-02T17:45:23Z<p>Kmacpher: /* Updated Tools */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Website Updates==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===Variant Information in Sequence Tab===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400240SGD Newsletter, Fall 20182018-10-02T17:41:34Z<p>Kmacpher: /* SGD at Yeast Genetics Meeting 2018 */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz Award]. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400239SGD Newsletter, Fall 20182018-10-02T17:41:01Z<p>Kmacpher: /* Mike Cherry Receives Ira Herskowitz Award */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the Ira Herskowitz Award]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the [http://conferences.genetics-gsa.org/yeast/2018/invited-speakers Ira Herskowitz] Award. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400238SGD Newsletter, Fall 20182018-10-02T17:38:41Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the Ira Herskowitz Award]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the Ira Herskowitz Award. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400237SGD Newsletter, Fall 20182018-10-02T17:38:09Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6.png|thumb|right|upright=1.0|The [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 CDC6] locus page today (right).]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the Ira Herskowitz Award]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the Ira Herskowitz Award. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=File:cdc6.png&diff=400236File:cdc6.png2018-10-02T17:36:40Z<p>Kmacpher: </p>
<hr />
<div></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400235SGD Newsletter, Fall 20182018-10-01T23:10:16Z<p>Kmacpher: /* Disease Data Now Available */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6-old.jpg|thumb|right|upright=.6|The CDC6 locus page from 1994]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the Ira Herskowitz Award]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the Ira Herskowitz Award. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|link=https://www.yeastgenome.org/complex/CPX-1042|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpherhttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_Fall_2018&diff=400234SGD Newsletter, Fall 20182018-10-01T23:09:23Z<p>Kmacpher: </p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the September 2018 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==25th Anniversary of SGD==<br />
[[File:cdc6-old.jpg|thumb|right|upright=.6|The CDC6 locus page from 1994]]<br />
<br />
<br />
SGD is proud to celebrate our 25th anniversary! Initiating in 1993 with AceDB and later launching as a website in 1994, SGD is among the oldest biological resources on the web. The SGD website started with the basics–just check out the old CDC6 locus page! In the decades since, SGD has grown to become the premier genetics and genomics resource for ''S. cerevisiae''. <br />
<br />
<br />
We wish to extend a big thank you for helping us make these past decades of service to the yeast community possible. [https://twitter.com/search?q=%23apoyg #APOYG!]<br />
<br />
<br><br><br />
<br />
==SGD at Yeast Genetics Meeting 2018==<br />
From August 22-26, 2018, the SGD team was out in full force at the Yeast Genetics Meeting in Stanford, CA. Here are some of the highlights from this awesome meeting:<br />
[[File:Mike-Award.jpg|thumb|right|upright=.8|Mike Cherry accepts the Ira Herskowitz Award]]<br />
===Mike Cherry Receives Ira Herskowitz Award===<br />
For his outstanding contributions in the field of yeast research in the last few decades, Mike Cherry, PI of SGD, received the Ira Herskowitz Award. Congratulations Mike!<br />
<br />
===Workshop: Getting More out of SGD===<br />
At our workshop, we talked about new features, cool tools, and some of the many ways you can access data at SGD to support your research. Check out the links below to download presentations given by SGD staff:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Presentation Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[Tools & Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_PN.pdf Looking at Loci with SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_workshop_EDW.pdf Finding Data(files) at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Alliance]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Posters===<br />
Below is a collection of posters SGD staff presented at the Yeast Genetics Meeting. Click on any of the links below to download the poster.<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Suzi Aleksander<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/5/5f/YGM2018_SA.pdf The Use of the Gene Ontology to Describe Biological Function at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Barbara Dunn<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/YGM2018_BD.pdf Beyond S288C: Incorporating new ''S. cerevisiae'' strain genomes and their associated not-in-S288C ORFs into SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[Updated regulation curation model at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Felix Gondwe<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/29/YGM2018_FG.pdf Downloading Data from SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kalpana Karra<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e2/YGM2018_KK.pdf YeastMine: An Advanced Search and Analysis Tool for SGD Data]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Rob Nash<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/38/YGM2018_RN.pdf Associating Yeast Genes with Human Disease-related Genes at SGD]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Patrick Ng<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/e/e8/YGM2018_PN.pdf Comparative Genomics at the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Ajay Shrivatsav VP<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/2/2d/YGM2018_ASVP.pdf SGD Migration to AWS Architecture]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Travis Sheppard<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/a/a4/YGM2018_TS.pdf Getting Data: API Access to SGD and The Alliance of Genome Resources]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Edith Wong<br />
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/34/Yeast2018_EDW_final.pdf Forming Protein Complex Pages at the ''Saccharomyces'' Genome Database]<br />
|-<br />
|}<br />
[[File:sgd-booth1.jpg|thumb|right|upright=.7|Staff members at the SGD booth]]<br />
<br />
===Fun Stuff===<br />
A big thank you to all who stopped by our booth! Visitors received all sorts of informational handouts and fun prizes, such as a SuperBud yeast toy. Many were also up to the challenge of completing our Yeast Genetics Crossword puzzle… and to the victors went the spoils of an awesome 25th anniversary SGD T-shirt!<br />
<br />
[[File:prizes.jpg|thumb|left|upright=.7|Look at all this cool stuff!]]<br />
<br />
<br><br><br />
<br />
We are always interested in answering questions and meeting the researchers and users that make up our community. We appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our booth, please feel free to share any comments or suggestions by [mailto:sgd-helpdesk@lists.stanford.edu contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23Yeast18&src=typd #Yeast18] on Twitter.<br />
<br />
<br />
<br />
<br><br><br />
[[File:sgd-api-access.jpg|thumb|upright=.4|Python examples for accessing SGD API]]<br />
==SGD API Examples==<br />
Did you know that SGD has a collection of python scripts which demonstrate how to access data from the SGD API? The collection can be found on our GitHub here: https://github.com/yeastgenome/sgd_api_examples<br />
<br><br><br />
<br />
<br />
<br />
==Disease Data Now Available==<br />
[[File:cancer_page.jpg|600px|link=https://www.yeastgenome.org/disease/DOID:162]]<br />
<br><br />
[[File:ccc2_disease.gif|thumb|right|link=https://www.yeastgenome.org/locus/S000002678/disease|upright=1.0|The [https://www.yeastgenome.org/locus/S000002678/disease CCC2 Disease Summary page].]]<br />
<br />
<br />
<br />
<br />
<br />
In our effort to promote the use of yeast as a catalyst for biomedical research, SGD has recently released new our Disease Pages. Each disease page corresponds to a [http://www.disease-ontology.org/ Disease Ontology] term, such as [https://www.yeastgenome.org/disease/DOID:162 cancer], and lists out all yeast genes that have a human homolog implicated in the disease.<br />
<br />
Yeast genes with human homologs implicated in disease will also have a new Disease Summary tab (example: [https://www.yeastgenome.org/locus/S000002678/disease CCC2]). All associated diseases are shown, along with a network diagram that relates yeast genes, their human homologs, and the diseases associated with the human homologs.<br />
<br />
For more information, be sure to check out our [https://sites.google.com/view/yeastgenome-help/function-help/disease-ontology-do Disease Ontology help page]. Check out the new pages, and be sure to let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu questions or comments!]<br />
<br><br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[File:complex_page.jpg|thumb|right|450px|The [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 Transcription Regulation Complex] page]]<br />
<br />
==Complex Pages Now Live==<br />
<br />
In addition to the new Disease data described above, SGD has also released our new Complex pages! Complex pages (example: [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex] provide manually curated information about the complex as well as helpful links and diagrams. Information contained within our Complex pages includes:<br />
<br />
*Manually curated summaries of the complex's function and biology<br />
*A list of all subunits and other complex participants<br />
*A Complex Diagram that shows the physical interactions between each subunit<br />
*Gene Ontology (GO) terms annotated to the complex<br />
*Images of complex structure from the [https://www.rcsb.org/ Protein Data Bank], if available<br />
*A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits<br />
<br />
Complex pages can be accessed by visiting the gene pages of its subunits. For example, to visit the [https://www.yeastgenome.org/complex/CPX-1042 GAL3-GAL80 complex page], go to the [https://www.yeastgenome.org/locus/S000002416#complex GAL3] or [https://www.yeastgenome.org/locus/S000004515#complex GAL80] gene page and find the Complex section.<br />
<br />
Be sure to check out the page for your favorite complex, and let us know if you have any [mailto:sgd-helpdesk@lists.stanford.edu feedback or questions].<br />
<br />
<br />
<br><br><br />
<br />
==Updated Tools==<br />
You may have noticed that a lot of SGD tools and features have been getting big updates. Here are some of the latest updates you can try out and explore:<br />
===New and Improved Gene Sequence Resources===<br />
SGD's [https://www.yeastgenome.org/seqTools Gene/Sequence Resources (GSR)] tool is a great way to figure out which tools at SGD can help you get information on the yeast genome. Given a chromosomal region, or raw DNA/protein sequence, GSR retrieves a list of sequence analysis tools, options for accessing biological information, and table/map displays. We’ve recently updated Gene/Sequence Resources to expand its search capabilities and provide more options for downloading, analyzing, and comparing sequences from different ''S. cerevisiae'' strains. New features in Gene/Sequence Resources include:<br />
<br />
*Options to select up to 11 different yeast strains for gene searches and sequence downloading<br />
*Ability to search for multiple genes at a time<br />
*Sequence alignment/variation tools such as Variant Viewer<br />
*Convenient, automatic loading of your sequence/gene of interest into other tools at SGD<br />
<br />
===Primer Design Update===<br />
We have also updated our [https://www.yeastgenome.org/primer3 Primer Design] tool to be based on the widely-used [http://primer3.ut.ee/ Primer3] package. It's easy to use the new [https://www.yeastgenome.org/primer3 Primer Design]. All you need to specify is the following:<br />
*A yeast gene name or DNA sequence of your choosing<br />
*A target region to create primers for<br />
*Optional parameters: primer length, GC content, melting temperature, and annealing. SGD has default values pre-set for these parameters, which you can change at any time.<br />
<br />
For more information, be sure to check out the Primer Design [https://sites.google.com/view/yeastgenome-help/analyze-help/primer-design help page].<br />
<br />
===Upgraded GO Term Finder===<br />
When you've got a list of genes and want to figure out how all the genes relate to each other in terms of their molecular functions, biological processes, or cellular components, SGD's [https://www.yeastgenome.org/goTermFinder GO Term Finder] is the place to go. We've recently upgraded our GO Term Finder to be much faster and more flexible than before. Give our upgraded [https://www.yeastgenome.org/goTermFinder GO Term Finder] a spin and let us know if you have any feedback!<br />
<br />
===New Interaction Summaries===<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
<br />
*[https://www.yeastgenome.org/blog/resistance-is-not-futile-how-yeasts-avoid-getting-ill-from-iils Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs] [https://www.yeastgenome.org/reference/S000217521 Higgins and colleagues] uncover ways to render yeast resistant to ionic liquids, paving the path for more efficient biofuel production.<br />
*[https://www.yeastgenome.org/blog/mixing-mitochondria-makes-magic Mixing Mitochondria Makes Magic] [https://www.yeastgenome.org/reference/S000209950 Wolters and coworkers] show that many yeast cells recombine mitochondrial DNA after mating, for better or for worse.<br />
*[https://www.yeastgenome.org/blog/too-much-of-a-good-thing-can-be-hazardous-to-your-health Too Much of a Good Thing Can Be Hazardous to Your Health] [https://www.yeastgenome.org/reference/S000216638 Chakraborty and colleagues] reveal that making too much of DNA mismatch repair proteins can be disastrous for your DNA and your health.<br />
*[https://www.yeastgenome.org/blog/almost-all-hands-on-deck-for-calcineurin (Almost) All Hands on Deck for Calcineurin] [https://www.yeastgenome.org/reference/S000216853 Connolly and colleagues] uncover the roles of the four mysterious "arms" of the yeast calcineurin protein, [https://www.yeastgenome.org/locus/S000001673 Cnb1p.]<br />
*[https://www.yeastgenome.org/blog/chaperone-wars-the-last-co-chaperone Chaperone Wars: The Last Co-chaperone] [https://www.yeastgenome.org/reference/S000217313 Reidy and coworkers] show that Sti1p helps save the galaxy by helping a protein chaperone perform its function and interact with other proteins.<br />
<br />
==What else have we been up to lately?==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.80]]<br />
You may have seen SGD representatives at the following meetings:<br />
<br><br><br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br />
<br />
*Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.<br />
<br />
<br><br><br><br />
<br />
==20th Anniversary of the Gene Ontology==<br />
<br />
==Upcoming Meetings==<br />
<b>[http://www.issy34-bariloche.com International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 1 - 4, 2018<br><br />
<br />
<b>[http://www.issy34-bariloche.com International Workshop on Brewing Yeasts]</b><br><br />
Bariloche, Patagonia, Argentina<br><br />
October 5 - 6, 2018<br><br />
<br />
<b>[https://www.embl.de/training/events/2018/EAE18-01/ EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]</b><br><br />
Heidelberg, Germany<br><br />
October 17 - 20, 2018<br><br />
<br />
<b>[http://conferences.genetics-gsa.org/fungal/2019/index 30th Fungal Genetics Conference]</b><br><br />
Asilomar Conference Grounds, Pacific Grove, CA, USA<br><br />
March 12 - 17, 2019<br></div>Kmacpher