December 08, 2020
This is the Fall 2020 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.
Contents:
We are pleased to announce that SGD’s brand new Allele Pages are now available on our website. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. These pages are still being updated with new information as it becomes available. The type of information that you can find on each allele page includes:
If you are interested in viewing all alleles for a specific gene or would like to view a comprehensive list of the alleles that SGD currently has curated, you can use this YeastMine template with your customized parameters.
SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page. Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016) .
Previously, the ‘Comparative Info’ section on the Gene Summary page contained a link to the Alliance of Genome Resources if integrated model organism details were available. Now, users will instead find hexagonal buttons representing each model organism (human, mouse, rat, zebrafish, fly, and worm) for which there is homologous gene information at the Alliance of Genome Resources. Clicking on the link will immediately direct the user to the gene page for the selected model organism on the Alliance website.
The Alliance of Genome Resources , a collaborative effort from SGD and other model organism databases (MOD), released version 3.2 in October. Notable improvements and new features include:
Jeremy Thorner, a prolific yeast researcher and outstanding mentor, has announced that his lab is closing. His lab provided the following notice:
“After 47 years at the University of California, Berkeley, the laboratory of Professor Jeremy Thorner will be closing permanently, as of 30 June 2021. After that date, there will be no way to distribute any strains, plasmids, enzymes, or antibodies generated during the course of the studies on Saccharomyces cerevisiae conducted by the Thorner laboratory over those many years.”
YeaZ is a system for efficiently and accurately segmenting microscopy images of yeast cells. It contains a convolutional neural network, with an underlying training set of high-qual|ty segmented yeast images, as well as a graphical user interface and a web application to employ, test, and expand the system. The system contains a Python based application with graphical user interface available on GitHub , as well as standalone apps for both Windows and Mac based computers, and training sets. Additional information is available in the accompanying Nature Communications paper by Dietler et al., 2020 .
YeaZ was created at École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland. Please contact Sahand Jamal Rahi with questions, or ideas for improvements.
It was with great sadness that we learned that Angelika Amon, cell biologist and Professor of Biology at MIT and a member of the Koch Institute for Integrative Cancer Research, passed away on October 29, 2020. Angelika was widely known for her novel contributions to the field of cell biology and proliferation, with her research focusing on aneuploidy and the consequences of chromosome mis-segregation. At the beginning of Angelika’s career, her work on yeast genetics led to the discovery that cyclins must break down completely before cells progress from mitosis to G1.
Her research has helped shape the current understanding of cell division, and her passion for genetics will live on through her students and colleagues who continue her work. Angelika was a treasured part of the genetics community and will be missed dearly.
The Genetics Society of America has featured a tribute piece in remembrance of Angelika Amon , written by her friend and colleague, Orna Cohen-Fix.
From October 6th-8th, PI Mike Cherry, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Gene Ontology Consortium meeting. Suzi presented on SGD’s GO display and GO tools, and curators learned more about how other databases utilize GO. SGD Curators also participated in meaningful discussions about improving existing GO resources while also helping with the planning of new GO projects.
We would like to thank The Gene Ontology for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!
We would like to take this opportunity to recognize that 2020 has brought many changes and challenges for everyone. Our thoughts go out to all those who have been impacted by the unprecedented events of this year.
We wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for three weeks starting on December 14 and will reopen on January 4th, 2021 . 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.
Categories: Newsletter
June 08, 2020
This is the Summer 2020 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.
Contents:
Are you away from the bench right now and have a bit of extra time on your hands? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD’s simple “Submit Data” form (https://www.yeastgenome.org/submitData).
Members of the SGD team virtually attended The Allied Genetics Conference in April 2020. Principal investigator Mike Cherry, PhD, gave a virtual workshop on using SGD and highlighted some of the useful tools and resources available to our users. SGD staff interacted with members of the yeast community through the conference Slack channels and also presented posters as part of the virtual poster sessions throughout the week (see below). We would like to thank the GSA for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!
Presenter | Poster Title |
Suzi Aleksander | “The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database” |
Micheal Alexander | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
Joanna Argasinska | “Saccharomyces Genome Database (SGD) Through the Years” |
Stacia Engel | “SGD & the Alliance of Genome Resources” |
Rob Nash | “Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes” |
We recently added the new ‘Explore SGD’ button to the SGD homepage which allows for the exploration of data and pages without an initial search query.
If you select the ‘Explore SGD’ button, you will be redirected to our search results page and can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike. New users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories.
Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website.
What are the basic features of SGD? Watch our new video to learn some of the key features that are available to help users with their research efforts. While this video does not include all of the many tools and resources that SGD has to offer, we have also generated a list of helpful SGD links which can be found on our help pages.
You can find this video, as well as other video tutorials on SGD resources, on our YouTube channel!
SGD is now uploading and storing supplemental materials for our yeast papers! We are hosting data from past, present, and future papers on our literature pages. To access these data, simply search SGD with the paper’s PubMed ID and then look for the “Downloadable Files.”
Happy Birthday (Bud-day!) to Us! May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all! In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast. We’ve grown a lot since then, and have even migrated to the cloud! But as always, we’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 26 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.
We recognize that 2020 has brought many changes and challenges. Our thoughts go out to all those impacted by the novel coronavirus, SARS-CoV-2. Like many of you, we have found ourselves adjusting to these times, and the SGD team is currently working from home for the foreseeable future. Rest assured, we are still working just as hard to maintain the SGD resource and continuing to serve the amazing budding yeast community!
Categories: Newsletter
December 05, 2019
This is the Fall 2019 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.
Contents:
From August 18th-22nd, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientists Barbara Dunn, Edith Wong, and Rob Nash, Biocuration Scientist Suzi Aleksander, Software Developer Felix Gondwe, and Associate Biocuration Scientist Patrick Ng attended the 29th International Conference on Yeast Genetics and Molecular Biology in Gothenburg, Sweden. Our attending staff presented at a workshop and poster sessions at the meeting, and presentation materials are downloadable at the links below. We had a great time interacting with users and getting their feedback on how to improve SGD as a resource for the budding yeast community.
Presenter | Presentation Title |
Mike Cherry | “Introduction to SGD Workshop” |
Stacia Engel | “SGD’s Collaboration with the Alliance of Genome Resources” |
Rob Nash | “Disease Associations and Protein Abundance” |
Edith Wong | “Macromolecular Complexes and Chemical Pages at SGD” |
Suzi Aleksander | “Gene Ontology at SGD: GO Slim Mapper” |
Patrick Ng | “Depicting the S288C Transcriptome at SGD” |
The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 2.3 in November. Notable improvements and new features include:
SGD recently updated the YeastPathways resource, containing more than 200 biochemical pathways, with help from the BioCyc group at SRI to provide an updated web portal and tools. You can query for metabolic network, pathway, enzyme, or metabolites, as well as access pathways from SGD’s Function menu or locus pages for genes with enzymatic roles.
Sequence tracks that depict single nucleotide polymorphisms and small insertion/deletions mapped relative to the reference strain S288C by Song et al. 2015 in 25 S.cerevisiae strains are now viewable in SGD JBrowse. They are accessible from the “variants” category when you click the “Select tracks” tab on the upper-left hand of the page.
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 24. 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.
The Allied Genetics Conference – TAGC 2020
Metro Washington, DC
April 22 to April 26, 2020
15th International Congress on Yeasts
University of Vienna, Vienna, Austria
August 23 to August 27, 2020
The 31st Fungal Genetics Conference
Asilomar Conference Grounds, Pacific Grove, CA
March 09 to March 14, 2021
Categories: Newsletter
June 03, 2019
This is the Spring 2019 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.
Contents:
SGD members in front of the 150-foot-diameter Stanford Dish.
Wednesday, May 8th, marked the 25th year that the SGD website has been live. Although we celebrated the 25th anniversary of the database last year, the actual website wasn’t online until the following year (when the “World Wide Web” had only been in existence for about 22 months). Starting in 1994, you could simply access SacchDB from our old server genome-www.stanford.edu to find information on your favorite model organism. We’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 25 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.
SGD staff celebrated the day by taking a tour around the Stanford campus and enjoying the beautiful California spring weather. Did you catch our throwback page for CDC6?
We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.
SGD has also updated our JBrowse with an additional 157 new data tracks related to genome-wide experiments and omics data for you to explore. The categories added include: Transcription & Transcriptional Regulation; Histone Modification; Chromatin Organization; RNA Catabolism; Transposons; DNA Replication, Recombination, and Repair.
SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell. Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85).
Two new YeastMine templates have been created to provide access to these data: Gene → Protein Abundance and Gene → Median Protein Abundance.
In March, the Alliance released version 2.1. The release showcases the combined effort from SGD and the other core Alliance members. Notable improvements and new features include:
From April 7th-10th, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the International Society for Biocuration’s 12th International Biocuration Conference in Cambridge, UK. Several of our staff presented posters, while Edith also gave a great talk on her recent Database publication: Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Below are the posters and the talk SGD staff presented at Biocuration 2019. Click on any of the links to download the presentation.
Presenter | Presentation Title |
Edith Wong | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
Presenter | Poster Title |
Suzi Aleksander | “In the Know About GO: A Newly Redesigned Website for the Gene Ontology” |
Felix Gondwe | “Downloading Data from SGD” |
Edith Wong | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
You might see some of our SGD members at these upcoming events:
Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual Yeast Genetics & Genomics course at Cold Spring Harbor Laboratory July 23 – August 12, 2019.
SGD will be attending ICYGMB2019, the 29th International Conference on Yeast Genetics and Molecular Biology in Göteborg, Sweden August 18-22, 2019. If you’re going, be sure to attend the SGD Workshop on the afternoon of Day 4, Wednesday August 21!
Kevin MacPherson telling the SGD classic about ‘why did the yeast cross the road?’ at the Fungal Genetics Conference. [Photo by Matt Sachs, GSA]
Presenter | Poster Title |
Barbara Dunn | “Associating Yeast Genes with Human Disease-related Genes at SGD” |
Kevin MacPherson | “Comparative Genomics at the Saccharomyces Genome Database” |
Categories: Newsletter
October 05, 2018
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Fall 2018 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
May 01, 2018
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This April 2018 newsletter is also available on the community wiki.
Categories: Newsletter
December 21, 2017
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2017 newsletter is also available on the community wiki.
Categories: Newsletter
December 20, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
August 29, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This August 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
March 15, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This March 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter