SGD Quarterly Newsletter, Winter 2012

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About this newsletter:

This is the Winter 2012 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

Contents

SGD Website Updated

Welcome to SGD's new look! All of the information and functionality you are familiar with at SGD is still available, but has been repackaged in order to provide better access to data and to provide additional tools and services. One exciting new feature is the SGD blog where we will highlight and discuss research articles and topics. To fully access the updated SGD site, you may need to clear the cache on your browser. We encourage you to explore the new site and send us feedback.

Message from SGD P.I., Mike Cherry

Thank you to those who have shared your thoughts and comments about the new site. I am very proud of our new look and all the features it incorporates. For the past year we worked with web design professionals and conducted studies to determine an optimal design for the SGD pages. Since the inception of SGD, the standards for computer-human interfaces and website usability have advanced and we realize that we must embrace these changes in order to reach out to all communities that depend on SGD. The new pages address many previously identified issues and the new design allows the 21,000 weekly users of SGD to more effectively find the information they require. In addition to providing a modern look, the new design greatly decreases the learning curve for new users.
I am delighted that our Search has been enhanced to provide auto-suggest and auto-complete features. The new Search interface gives access to more types of information and facilitates the discovery of huge amounts of information integrated at SGD. Easier access to all the data is also facilitated by recent tool enhancements and data additions. Over the past year several hundred new datasets have been added to the Genomic Browser and we will continue to add new data at about the same rate. This year will also see the addition of new types of data, in particular strain genomic sequence.
I appreciate that change can be difficult. I hope that adjusting to the new site will not be too onerous and, in addition to the data which you are accustomed to getting from the site, you will discover new datatypes useful to you that you may not have realized were contained within SGD. I thank you again for providing me feedback on the new and more powerful SGD and ask that you please continue to send questions and comments to the SGD HelpDesk.
Wishing you all the best in 2012,
Mike
J. Michael Cherry, Ph.D.
Associate Professor (Research)
Department of Genetics
Stanford University
Stanford, CA 94305-5120

Short Video Tutorials for Using SGD Tools

SGD is developing a library of short video tutorials designed to introduce you to the new website organization and to step you through using various SGD tools. The list of tutorials currently available is located on our SGD Video Tutorials page. The video YeastMine is Awesome! describes just a few of the many "awesome" things you can do in YeastMine. See other tutorials for more detailed explanations of how to use these and many other cool features of SGD.

Filter Expression Data by Experimental Condition

Expression analysis at SGD now offers the ability to filter datasets by condition(s) or process(es) studied. A set of controlled vocabulary (CV) terms describing various perturbations associated with microarray experiments has been constructed and defined, and these terms have been used to tag the comprehensive collection of almost 400 datasets now available in SGD's instance of SPELL (Serial Pattern of Expression Levels Locator). In this manner, datasets displayed in search results can be filtered using tags (CV terms) such as "oxidative stress" or "sporulation." Filtering is an option for the "New Search," "Show Expression Levels," and "Dataset Listing" features. The SPELL interface has been provided through a collaboration with the SGD Colony at Princeton University. Special thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help in implementing the dataset tag filtering option for SPELL at SGD.

Download and Analyze S. cerevisiae Strain Sequences

SGD now has available ORF DNA and protein sequence alignments for dozens of S. cerevisiae strains. The alignments are accessible via a new 'Analyze Sequence' section on the Locus Summary pages, along with options for retrieval and download of the sequences. The BLAST Search and Pattern Matching (PatMatch) tools have also been updated to include genomic, coding, and protein sequences from 28 additional S. cerevisiae strains. Stay tuned in the coming months as SGD continues to add new strains and to develop additional tools for viewing and analysis of these sequences.

GO Slims Updated

SGD has updated its Yeast Molecular Function and Biological Process GO Slims to include additional terms. The Yeast GO Slims are a set of GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, "granular" gene annotations to more general "high-level" terms. These terms have been selected by SGD curators based on annotation statistics and biological significance. To complement the expanded Yeast GO Slims, we have also added "generic GO-Slim" options to our GO Slim Mapper tool. The generic GO-Slim is developed and maintained by the Gene Ontology Consortium and includes fewer and higher-level terms than those provided by the Yeast GO-Slim.

The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and YeastMine. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the downloads site.

New Data Tracks Added to GBrowse

SGD has added a mélange of data tracks to our GBrowse genome viewer from six publications covering various applications of high-throughput sequencing, including genome-wide distributions of DNase I-protected genomic footprints (Hesselberth et al. 2009), recombination-associated double strand breakpoints (Pan et al. 2011), polyadenylation sites (Ozsolak et al. 2010), antisense ncRNAs (Yassour et al. 2010), cryptic unstable transcripts (CUTs) (Neil et al. 2009) and Xrn1-sensitive unstable transcripts (XUTs) (van Dijk et al. 2011). You can now also easily download data tracks, metadata and supplementary data by clicking on the '?' icon on each data track within GBrowse. Please watch our video tutorial for more information on how to download data from GBrowse. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!

SGD Downloads Site Updated

SGD has updated its file Downloads Site. The new look includes complete genomic and protein sequence files for the current S288C reference sequence (Release 64) and all previous releases. Genomic sequence and annotation for numerous S. cerevisiae strains are also available for download. As always we make available many other published datasets and a large collection of information curated by SGD from the literature.

Updated Resource: YPL+

Links to YPL+ (the Yeast Protein LocalizationPlus Database) have been added to the "Protein Information" section of SGD Locus Summary pages. YPL+ is a recently upgraded version of the YPL image database, and has been expanded to include GFP-localization data for more than 3500 genes. Data in YPL+ are derived from a collection of GFP fusion constructs generated by C-terminal chromosomal tagging (Huh et al., 2003, Nature 425, 686-691) as well as a collection of proteins involved in lipid metabolism, constructed by in vivo recombination (Natter et al., 2005, Mol. Cell. Proteomics 4(5), 662-672). Thanks to Sepp Kohlwein for help in setting up these links.

New Look and Features for Yeast Biochemical Pathways

SGD has upgraded Yeast Biochemical Pathways (YeastCyc) to Pathway Tools Version 15.0. This version gives the pathway database a new look and offers new features for querying and analyzing data. A pathway-specific toolbar, available on each pathway web page, provides easy navigation and new features, including options to highlight pathways and substrates on the cellular overview and to download a list of genes from a specific pathway. Pathway files (yeastcyc15_201109.tar.gz and biochemical_pathways.tab) can be downloaded from SGD's downloads page.

YEASTBOOK now available!

YEASTBOOK is now available in the November 2011 issue of GENETICS. This month's issue includes a Perspectives article by David Botstein and Gerry Fink, a review about transcriptional regulation written by Steve Hahn and Elton Young, and a review about sporulation written by Aaron Neiman. Edited by Alan G. Hinnebusch, YEASTBOOK will be a compendium of comprehensive reviews that provides the current state of knowledge of the molecular biology, cellular biology, and genetics of Saccharomyces cerevisae. Approximately 50 YeastBook review articles will be published in GENETICS (a peer-edited journal of the Genetics Society of America) over the next two years. Gene names mentioned in YEASTBOOK reviews are linked back to SGD.

Upcoming Conferences and Meetings

  • 19th Annual Southeastern Regional Yeast Meeting
Emory University, Atlanta, GA
February 24-26, 2012
  • Fifth International Biocuration Conference*
Georgetown University Conference Center, Washington D.C.
April 2-4, 2012
  • 10th Francophone Yeasts Meeting, Levures, Modele et Outlis-10
University of Toulouse, France
April 2-4, 2012
  • Model Organisms to Human Biology: Cancer Genetics*
Omni Shoreham, Washington, D.C.
June 17-20, 2012
  • Yeast Genetics 2012*
Princeton University, New Jersey, USA
July 31 - August 5, 2012
  • 13th International Congress on Yeasts
Madison, WI, USA
August 26-30, 2012
  • 9th International Meeting on Yeast Apoptosis
Rome, Italy
September 16-20, 2012
  • Experimental Approaches to Evolution and Ecology using Yeast
EMBL Heidelberg, Germany
October 17-21, 2012


*asterisks indicate attendance by SGD

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