SGD Newsletter, Summer 2022

About this newsletter:
This is the Summer 2022 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. You can view this newsletter as well as previous newsletters on our Community Wiki.

Performance updates at SGD

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Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the front end of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the back end, so we can improve our data uploads.

We hope to see improved performance for you, our users. And if you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

Research spotlights are back

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The back end of SGD involves “triaging” all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a blog post that appears on the SGD home page.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. Some of the most intriguing papers are shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.

Upcoming Yeast Genetics Meeting in person

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We may have forgotten how to talk to other people in person, but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the YGM website.

Congratulations to Jeremy Thorner

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal Biomolecules dedicated to his work. Special Issue: "Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner"

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

SGD collaborates with labs to integrate data

On this topic of integration, we have recently collaborated to bring datasets into SGD that came directly from labs, rather than from publications. We integrated the X set from Y lab, the XX set from the YY lab, and the ….. what else?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

Micropublications take off

We are seeing a strong set of Micropublications come through the database and are glad for this venue to publish small but useful findings. [What else to say??]

Alliance of Genome Resources - Recent Release

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 4.1 this past August. Notable improvements and new features included:

Upcoming Conferences and Courses

• • Cold Spring Harbor Laboratory, NY
  • July 26 - August 15, 2022
• Yeast Genetics Meeting - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
  • University of California, Los Angeles
  • August 17 – 21, 2022

Gene Ontology Consortium Fall 2022

From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:

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We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.