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.
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.
|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”|
|Barbara Dunn||“Beyond S288C: Incorporating Genomic Sequence Information from Large-Scale S. cerevisiae Population Surveys into SGD”|
|Felix Gondwe||“Downloading Data from SGD”|
|Edith Wong||“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”|
|Patrick Ng||“Representing Transcriptional Heterogeneity and Inter-Strain Variation at the Saccharomyces Genome Database”|
|Stacia Engel||“SGD & the Alliance of Genome Resources”|
|Suzi Aleksander||“The Use of the Gene Ontology to Describe Biological Function at SaccharomycesGenome Database”|
|Rob Nash||“Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes”|
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