SGD Newsletter, 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
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
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
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):
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:
- Yeast Reveals a Vicious Circle Between Sugar and Cancer Peeters and coworkers used budding yeast to investigate the Warburg effect relating to cancer aggressiveness and the consumption of sugar.
- Something from Nothing: A New, Structured Protein from Noncoding DNA Bungard and colleagues looked into protein formation from noncoding intergenic DNA.
- Transcription Factors: Kings of the Genome Jungle Wollman and colleagues show that two transcription factors in yeast "swing" across DNA segments through a process called intersegment transfer.
- Divide and Prosper Hanner and Rusche explore the idea of subfunctionalization, like a swiss army knife, using S. cerevisiae proteins Sir3p and Orc1p.
- Cheerio Containment Lawrence and coworkers look at how well Histone H1 can bind to DNA as a mechanism for gene expression regulation.
Recent Publications from SGD Staff
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:
- Senior Biocuration scientist Terry Jackson and Biocuration Assistant Kevin MacPherson attended the Fungal Genetics Meeting in March 2017.
- PI Mike Cherry and all SGD Senior and Assistant Biocuration Scientists attended the 10th International Biocuration Conference in March 2017 at Stanford University.
- Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July 2017.
- PI Mike Cherry and Senior Biocuration Scientists Stacia Engel and Edith Wong attended and conducted an SGD workshop (see photo below) at the 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) in late August 2017.
Happy Holidays from SGD!
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.
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 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
October 17 - 20, 2018