SGD Quarterly Newsletter, Fall 2010

About this newsletter:

This is the Fall 2010 issue of the quarterly 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 also subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

Yeast Biochemical Pathways Upgraded

The Yeast Biochemical Pathways have been upgraded to Pathway Tools version 14.0. This version offers a robust search system with auto-complete and filtering functionality to search for compounds, reactions, genes/proteins and pathways. In addition, the Advanced Query page has been enhanced to support structured queries to extract data. The yeastcyc14.0 data files that can be used with version 14.0 and the biochemical_pathways.tab file can be downloaded from SGD's downloads page. Other features of interest are:

1. Downloadable Yeast Biochemical Pathway Poster, which gives you an overview of the manually-curated pathways
2. The Comparative Analysis Tool, which allows you to make comparisons between different pathway databases, and compute summary statistics on a single database.

Pathways can be accessed through the advanced query page: http://pathway.yeastgenome.org/query.shtml and the biochemical_pathways.tab file can be downloaded at: http://downloads.yeastgenome.org/literature_curation/

SGD on Facebook and Twitter

SGD is now on Facebook and Twitter! 'Like' us on Facebook or follow @yeastgenome on Twitter to get updates about new features, tips on using SGD, and interesting tidbits about yeast.

FTP Site to be Retired

SGD's FTP site will soon be retired. All data files will still be available but access will now be through the web (HTTP).

Download data at: http://downloads.yeastgenome.org/

SGD Survey a Huge Sucess

SGD recently circulated a survey to obtain feedback from our community of users for an upcoming grant renewal. We had a tremendous response with over 1400 community members completing the survey, an increase of 500 compared to last year. Thanks to all of our users who completed this usage survey, providing us with valuable feedback.

Beta Release of YeastMine

Try the beta version of YeastMine for flexible queries and fast retrieval of chromosomal features, sequences, interactions, and GO- and phenotype-related annotations using predefined template queries or customized queries. New datatypes and additional templates will be added in the near future. YeastMine is part of a joint project with Intermine, the Rat Genome Database (RGD), and The Zebrafish Model Organism Database (ZFIN) to provide interoperability between the model organism databases via shared datatypes,such as Gene Ontology (GO) annotations or orthologs. Email us your comments and questions about YeastMine.

Try YeastMine at: http://yeastmine.yeastgenome.org:8080/yeastmine/

Exploratory Gene Association Networks (EGAN) Software

A new software tool has been developed for the visualization and interpretation of high-throughput exploratory assays. Designed for the bench biologist, EGAN is a downstream analysis/pathway/gene set enrichment/visualization tool that facilitates data-driven discovery of novel systems biology and disease pathways through the integration of computational analysis output with a gene-centric knowledge base.

A manuscript describing the software has recently been published by Paquette and Tokuyasu (Bioinformatics 26(2):285-6). Thanks to Jesse Paquette at UCSF for contacting us with information on this software.

For more information, please see the SGD wiki: http://wiki.yeastgenome.org/index.php/EGAN.

Reduce and Visualize Gene Ontology (REViGO) Web Server

A web server has been developed to aid in the visualization of Gene Ontology (GO) terms. With ReViGO long lists of GO terms generated from high-throughput experiments can be summarized by removing redundant terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, treemaps or tag clouds. Thanks to Fran Supek of the Rudjer Boskovic Institute for contacting us with information on this web server.

For more information, please see the SGD wiki: http://wiki.yeastgenome.org/index.php/REVIGO.

New Gene Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter new summary paragraphs have been added to their respective Locus Summary pages for 4 features.

Genes with new summary paragraphs are reported weekly on SGD's What's New page.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• From Functional Genomics to Systems Biology (EMBO conference series)

EMBL Heidelberg, Germany

November 13-16, 2010

• 26th Fungal Genetics Meeting (GSA)

Asilomar Conference Center, Pacific Grove, CA

March 15-20, 2011

• 52nd Annual Drosophila Research Conference (GSA)

Town & Country Resort & Conference Center, San Diego, CA

March 30 - April 3, 2011

• 8th International Meeting on Yeast Apoptosis (IMYA)

Canterbury, Kent, United Kingdom

May 2-6, 2011

• Telomeres & Telomerase

Cold Spring Harbor Labs, CSH, NY

May 3-7, 2011

• Omics Meets Cell Biology

Keystone Symposia, Alpbach, Austria

May 8-13, 2011

• The Biology of Genomes

Cold Spring Harbor Labs, CSH, NY

May 10-14, 2011

• International C. elegans Meeting (GSA)

UCLA, Los Angeles, CA

June 22-26, 2011

• 25th International Conference on Yeast Genetics and Molecular Biology

Olsztyn, Poland

July 11-16, 2011

• Yeast Cell Biology

Cold Spring Harbor Labs, CSH, NY

August 16-20, 2011

asterisks indicate attendance by SGD.*

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