Difference between revisions of "SGD Newsletter, December 2017"

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'''About this newsletter:''' <br>
 
'''About this newsletter:''' <br>
  
This is the December 2016 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.
+
This is the December 2017 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.
  
 
==SGD Moves to the Cloud==
 
==SGD Moves to the Cloud==
 +
[[File:Superbud_Cloud.png|thumb|left|upright=1.5]]
 +
We just completed a major database schema change and complete data migration to the Amazon Cloud (AWS). This new schema change is meant to improve database speed and stability to better serve our users and the yeast community.<br>
 +
<br>
 +
Because of the massive scale of the data migration, we had to temporarily freeze data curation during this transition. We are happy to announce that we are now back adding new literature to SGD! We are also updating colleague information and standardizing gene names that were published during the data freeze.<br>
 +
<br>
 +
We are very excited about the completion of this move to the cloud and the opportunity to improve SGD. Thank you so much for your patience during this major database change!<br>
 +
<br>
 +
<br>
  
 +
<br>
 
==Yeast Genetics Meeting 2018==
 
==Yeast Genetics Meeting 2018==
[[File:Yeast_Genetics_Meeting_GSA.png||thumb|left|upright=1]]
+
[[File:Yeast_Genetics_Meeting_GSA.png|thumb|left|upright=1.5]]
'''From the organizers:'''
+
The [http://conferences.genetics-gsa.org/yeast/2018/index Yeast Genetics Meeting] will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae [https://twitter.com/hashtag/APOYG?src=hash #APOYG]!. In addition to oral presentations, which are selected from the submitted abstracts, there will also be awards for the best posters. Abstract submission opens March 28, 2018 and ends May 17, 2018. This meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience.
<br>
 
"The [http://conferences.genetics-gsa.org/yeast/2018/index Yeast Genetics Meeting] will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae. Oral presentations are selected by the organizers from the submitted abstracts. The meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience.
 
  
We are pleased to announce the following awards and lectures will be presented at the meeting:
+
The following awards and lectures will be presented at the meeting:
  
:*Lee Hartwell Lecture: Fred Winston, Harvard Medical School
+
::*Lee Hartwell Lecture: Fred Winston, Harvard Medical School
:*Ira Herskowitz Award: Mike Cherry, Stanford University
+
::*Ira Herskowitz Award: Mike Cherry, Stanford University
:*Lifetime Achievement Award: Steve Oliver, University of Cambridge
+
::*Lifetime Achievement Award: Steve Oliver, University of Cambridge
:*Winge-Lindegren Address: Virginia Zakian, Princeton University
+
::*Winge-Lindegren Address: Virginia Zakian, Princeton University
:*Special Presentation: David Botstein, Calico
+
::*Special Presentation: David Botstein, Calico
Plan now to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. Present your research, re-connect with peers, and generate new approaches to your work."
+
<br>
<br><br>
+
Plan now to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. Registration opens April 4, 2018. We hope to see you there! [https://twitter.com/hashtag/YEAST18?src=hash #YEAST18]
 
 
Abstract submission opens March 28, 2018. We hope to see you there! [https://twitter.com/hashtag/APOYG?src=hash #APOYG]
 
  
 
==The ALLIANCE of Genome Resources==
 
==The ALLIANCE of Genome Resources==
[[File:alliance_logo.png|300px]]
+
[[File:alliance_logo.png|thumb|left|upright=1]]
 
+
The Alliance of Genome Resources (the Alliance) announces the release of the Alliance of Genome Resources website 1.0 – providing unified access to comparative genetics and genomics data from the Alliance data resources ([http://www.alliancegenome.org www.alliancegenome.org]). The focus of the Alliance is to facilitate the use of these data towards better understanding of human biology and disease as well as providing cross-species comparative information.<br>
 +
<br>
 +
As part of this initial release, Alliance working groups have focused on the ability to easily access pages that summarize details of genes and diseases, with extensive representation of orthology data, and with access to multi-track JBrowse capabilities primarily for visualization of sequence data. Users recover gene details, functional information, and disease associations within a comparative perspective. As the integration of the MOD and GO teams progress with inclusion of additional data, the vision going forward includes the incorporation of other model organism information resources and other bioinformatic nodes within a common data platform, facilitating data recovery, analysis, and integration.<br>
 +
<br><br>
 +
You may have noticed that links to the Alliance pages have been incorporated on the SGD Locus Summary Pages under "comparative info" (example below):<br>
 +
<br>
 
[[File:Alliance_Comp_Info.png|900px]]
 
[[File:Alliance_Comp_Info.png|900px]]
 +
<br><br>
 +
For more updates and announcements on the Alliance, check out the Alliance [https://www.facebook.com/alliancegenome/ Facebook page], or check out our twitter page [https://twitter.com/alliancegenome @alliancegenome].
 +
<br>
  
 
==Research Spotlight (Blog posts)==
 
==Research Spotlight (Blog posts)==
Line 50: Line 63:
 
You may have seen SGD representatives at the following meetings:
 
You may have seen SGD representatives at the following meetings:
 
*Senior Biocuration scientist Terry Jackson and Biocuration Assistant Kevin MacPherson attended the [http://www.genetics-gsa.org/fungal/2017/ Fungal Genetics Meeting] in March 2017.
 
*Senior Biocuration scientist Terry Jackson and Biocuration Assistant Kevin MacPherson attended the [http://www.genetics-gsa.org/fungal/2017/ Fungal Genetics Meeting] in March 2017.
*PI Mike Cherry and all Senior and Assistant SGD Biocuration Scientists attended the [http://med.stanford.edu/biocuration.html 10th International Biocuration Conference] in March 2017 at Stanford University.
+
*PI Mike Cherry and all SGD Senior and Assistant Biocuration Scientists attended the [http://med.stanford.edu/biocuration.html 10th International Biocuration Conference] in March 2017 at Stanford University.
 
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=17 Yeast Genetics and Genomics] course at CSHL in late July 2017.
 
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=17 Yeast Genetics and Genomics] course at CSHL in late July 2017.
*PI Mike Cherry and Senior Biocuration Scientists Stacia Engel and Edith Wong attended the [http://www.yeast2017.cz 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)] in late August 2017.
+
*PI Mike Cherry and Senior Biocuration Scientists Stacia Engel and Edith Wong attended, hosted a booth at (picture below), and conducted an SGD workshop at the [http://www.yeast2017.cz 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)] in late August 2017.<br>
 +
[[File:SGD_Prague_Booth.jpg|400px]]
  
 
==Happy Holidays from SGD!==
 
==Happy Holidays from SGD!==
Line 72: Line 86:
 
Stanford University, Palo Alto, California<br>
 
Stanford University, Palo Alto, California<br>
 
August 22 – 26, 2018<br>
 
August 22 – 26, 2018<br>
 +
 +
<b>[https://bio.kuleuven.be/pf/IMYA13 13th International Meeting on Yeast Ageing and Apoptosis]</b><br>
 +
The Irish College, Leuven, Belgium<br>
 +
August 26 – 30, 2018<br>
  
 
<b>[http://cms2.unige.ch/sciences/biologie/bimol/lmo13/ 13th Edition of the International Levures, Modèles et Outils (Yeasts, Models and Tools)]</b><br>
 
<b>[http://cms2.unige.ch/sciences/biologie/bimol/lmo13/ 13th Edition of the International Levures, Modèles et Outils (Yeasts, Models and Tools)]</b><br>

Latest revision as of 13:29, 19 December 2017

About this newsletter:

This is the December 2017 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.

SGD Moves to the Cloud

Superbud Cloud.png

We just completed a major database schema change and complete data migration to the Amazon Cloud (AWS). This new schema change is meant to improve database speed and stability to better serve our users and the yeast community.

Because of the massive scale of the data migration, we had to temporarily freeze data curation during this transition. We are happy to announce that we are now back adding new literature to SGD! We are also updating colleague information and standardizing gene names that were published during the data freeze.

We are very excited about the completion of this move to the cloud and the opportunity to improve SGD. Thank you so much for your patience during this major database change!



Yeast Genetics Meeting 2018

Yeast Genetics Meeting GSA.png

The Yeast Genetics Meeting will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae #APOYG!. In addition to oral presentations, which are selected from the submitted abstracts, there will also be awards for the best posters. Abstract submission opens March 28, 2018 and ends May 17, 2018. This meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience.

The following awards and lectures will be presented at the meeting:

  • Lee Hartwell Lecture: Fred Winston, Harvard Medical School
  • Ira Herskowitz Award: Mike Cherry, Stanford University
  • Lifetime Achievement Award: Steve Oliver, University of Cambridge
  • Winge-Lindegren Address: Virginia Zakian, Princeton University
  • Special Presentation: David Botstein, Calico


Plan now to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. Registration opens April 4, 2018. We hope to see you there! #YEAST18

The ALLIANCE of Genome Resources

alliance logo.png

The Alliance of Genome Resources (the Alliance) announces the release of the Alliance of Genome Resources website 1.0 – providing unified access to comparative genetics and genomics data from the Alliance data resources (www.alliancegenome.org). The focus of the Alliance is to facilitate the use of these data towards better understanding of human biology and disease as well as providing cross-species comparative information.

As part of this initial release, Alliance working groups have focused on the ability to easily access pages that summarize details of genes and diseases, with extensive representation of orthology data, and with access to multi-track JBrowse capabilities primarily for visualization of sequence data. Users recover gene details, functional information, and disease associations within a comparative perspective. As the integration of the MOD and GO teams progress with inclusion of additional data, the vision going forward includes the incorporation of other model organism information resources and other bioinformatic nodes within a common data platform, facilitating data recovery, analysis, and integration.


You may have noticed that links to the Alliance pages have been incorporated on the SGD Locus Summary Pages under "comparative info" (example below):

Alliance Comp Info.png

For more updates and announcements on the Alliance, check out the Alliance Facebook page, or check out our twitter page @alliancegenome.

Research Spotlight (Blog posts)

In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:

Recent Publications from SGD Staff

SuperYeast.jpg

1. Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2017) Saccharomyces Genome Database informs human biology. Nucleic Acids Res. 2017 Nov 11; pii:gkx1112. doi: 10.1093/nar/gkx1112. PMID: 29140510

2. Wong ED (2017) Exploring Protein Function Using the Saccharomyces Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13. PMID: 28365719

3. MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the Saccharomyces Genome Database. Database (Oxford). 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002. PMID: 28365719

4. Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the Saccharomyces Genome Database. Database (Oxford). 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. PMID: 28365727

What else have we been up to lately?

You may have seen SGD representatives at the following meetings:

SGD Prague Booth.jpg

Happy Holidays from SGD!

SnowShmoo.png


We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting on December 23rd, reopening on January 8th, 2018. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions.



Upcoming Meetings

South Eastern Regional Yeast Meeting (SERYM)
Rhodes College, Memphis TN
March 9 – 11, 2018

5th International Synthetic & Systems Biology Summer School - SSBSS 2018
Certosa di Pontignano (Siena) Tuscany, Italy
July 25 to 29, 2017
Application and abstract submission deadline: March 31, 2018

Yeast Genetics Meeting
Stanford University, Palo Alto, California
August 22 – 26, 2018

13th International Meeting on Yeast Ageing and Apoptosis
The Irish College, Leuven, Belgium
August 26 – 30, 2018

13th Edition of the International Levures, Modèles et Outils (Yeasts, Models and Tools)
Musikinsel, Rheinau, Switzerland
September 11-14, 2018

International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"
Bariloche, Patagonia, Argentina
October 1 - 4, 2018

International Workshop on Brewing Yeasts
Bariloche, Patagonia, Argentina
October 5 - 6, 2018

EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems
Heidelberg, Germany
October 17 - 20, 2018