SGD Quarterly Newsletter, Fall 2012

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About this newsletter:

This is the Fall/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 Hardware Update

We have been migrating SGD servers to new faster hardware! You may have already noticed an increase in performance.

SGD Servers Moved to new Data Center

Many SGD tools and resources were unavailable from Tuesday afternoon, November 27th, until Monday, December 3rd because we moved all of our servers to a new data center. This new data center provides a more secure facility, a faster network, and a backup generator to provide electricity in the event of a power failure. The main SGD database was available during this time, but many tools and pages were not, such as Pathways, YeastMine, Downloads/FTP, SPELL, GBrowse, Textpresso, and the SGD Wiki. This move is very significant for us, as we are now in a professionally managed computing facility with all the necessary backup cooling and power contingencies available. This move also allows us to continue expanding our services. The computer room is critical for the stability of SGD and other resources. Our previous location was created when SGD was young, and did not accommodate the amount of growth we have enjoyed. We are very happy to have the opportunity to be located in this brand new facility designed for research computing. We apologize for any inconvenience the downtime may have caused, and thank you for your patience during our move to the new data center.

New Strain Sequences Available

SGD has incorporated two new S. cerevisiae strain genomes: CEN.PK113-7D and ZTW1. CEN.PK113-7D is a laboratory strain derived from parental strains ENY.WA-1A and MC996A, and is popular for use in systems biology studies. ZTW1 was isolated from corn mash used for industrial bioethanol production in China in 2007. We have also incorporated an updated genomic sequence for W303-derivative K6001, a key model organism for research into aging. The previous version of W303 was an early view courtesy of Markus Ralser. SGD has updated the ORF DNA and protein sequence alignments to include these two additional strains, and the updated W303. We have also included the new genomic, coding, and protein sequences in both the BLAST Search and Pattern Matching (PatMatch) tools. The alignments are accessible via the Analyze Sequence section on the Locus Summary pages. Also available are retrieval and download options.

New Author Contact System

Many of you may have received emails from SGD inquiring about specific recent publications of yours. These are part of a new semi-automated system we are using to contact researchers who have published S. cerevisiae related papers within the last six months. Our hope for this system is that you, our colleagues, will help us prioritize papers that are rich in new information on S. cerevisiae genes, thereby streamlining our curation process. We very much appreciate all the responses that we have received so far - please keep them coming! You also don't need to wait for an email from us to send us comments on your publications. Contact SGD curators at sgd-helpdesk@lists.stanford.edu if you'd like to submit comments regarding a recently published paper, and we will send you a blank submission form.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available on the SGD Wiki.

  • British Yeast Group Meeting - BYG2013
Nottingham, UK
March 20-22, 2013
Stara Lesna, Slovakia
June 18, 2013
Frankfurt University, Frankfurt, Germany
August 29 - September 3, 2013


*asterisks indicate attendance by SGD

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