SGD Quarterly Newsletter, Spring 2012
About this newsletter:
This is the Spring 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
New Data Tracks Added to GBrowse
SGD has added a new mix of data tracks to our GBrowse genome viewer from seven publications covering transcriptome exploration via tiling microarrays (David et al. 2006), genomic occupancy of RNA polymerase II and III and associated factors (Kim et al. 2010; Ghavi-Helm 2008), 3'end processing (Johnson et al. 2011), histone H2BK123 monoubiquitination (Schulze et al. 2011) and high-resolution ChIP by a novel method called ChIP-exo (Rhee et al. 2011; Rhee et al. 2012). Download data tracks, metadata and supplementary data by clicking on the '?' icon for a given track within GBrowse or directly from the SGD Download page. 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!
Expression Data and LiftOver Files Available for Download
RNA expression data included in SGD's SPELL expression analysis tool are now available for download in the expression directory of SGD's Download page. Datasets are grouped by publication and provided in PCL format. LiftOver files that allow conversion of chromosomal coordinates between different S. cerevisiae genome versions are also now available for download via the genome_releases link in the sequence directory.
Yeast Genome App
SGD will soon release YeastGenome, an app for the iPhone, iPad and iPod. Use this app to search or browse information about your favorite genes including: gene names, descriptions, Gene Ontology annotations, phenotypes and interaction data. Save your favorite genes and email details to collaborators. See a description of the app at: http://www.yeastgenome.org/yeastgenome-app-information. This free app will be available from iTunes at: http://itunes.com/apps/yeastgenome.
Sequence Data for YKO and SGA Collection Progenitor Strains
SGD will soon have available ORF DNA and protein sequence alignments for BY4741 and BY4742, the progenitor strains used for the original yeast knockout (YKO) deletion collection and for synthetic genetic array (SGA) analysis. Alignments will be accessible via the 'Analyze Sequence' section on Locus Summary pages, along with options for retrieval and download of the sequences. The BLAST Search and Pattern Matching (PatMatch) tools will also be updated to include genomic, coding, and protein sequences from these strains. Thanks to Frederick Roth and his lab for making these sequence data available to the community.
Browsing Video Help
In the past several months SGD has put together ~20 video tutorials that either highlight new features and tools or describe how to use specific aspects of these tools. For quick visual help with tools such as YeastMine, GBrowse, Biochemical Pathways and the Expression tool SPELL, please visit the Video Tutorial section of our help pages and click on your favorite topic: http://www.yeastgenome.org/help/video-tutorials
Images for the SGD homepage
We hope that your transition to the new SGD site was relatively smooth and that you have been enjoying the new look and features. We welcome community contributions of your yeast images for the slideshow on our homepage. Send any high-resolution images you would like us to consider to: firstname.lastname@example.org.
What are Yeast
SGD has updated "What are yeast?", a page containing general information about yeast, its commercial applications, the use of yeast as a model organism, and links to some general resources for students, educators and others. This page and other helpful yeast resources can be found in the "General Topics" section of the SGD wiki by clicking on "Resources" under "Community" on SGD's main menu bar. Please take a look to find out more: http://wiki.yeastgenome.org/index.php/What_are_yeast%3F
SGD at YGM meeting
Registration for this year's Yeast Genetics and Molecular Biology Meeting is now open. Members of SGD will be attending the meeting hosted this year by Princeton University, July 31st through Aug. 5th, 2012. Come on by and visit us at the SGD table, or at one of our many posters. Can't make the meeting? Follow it and keep up with the latest science by following #YEAST2012 on Twitter
Upcoming Conferences and Meetings
Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings
- General Meeting of the American Society for Microbiology
- San Francisco, California
- June 16-19, 2012
- St. Feliu de Guixols, Girona, Spain
- June 16-21, 2012
- Omni Shoreham, Washington, D.C.
- June 17-20, 2012
- FASEB Conference: Yeast Chromosome Structure, Replication & Segregation
- Steamboat Springs, Colorado
- July 15-20, 2012
- Princeton University, New Jersey, USA
- July 31 - August 5, 2012
- Madison, WI, USA
- August 26-30, 2012
- 9th International Meeting on Yeast Apoptosis
- Rome, Italy
- September 16-20, 2012
- EMBL Heidelberg, Germany
- October 17-21, 2012
*asterisks indicate attendance by SGD
Manage your subscription
To SUBSCRIBE: If you think friends or colleagues would be interested in receiving this newsletter, they can subscribe by filling out an SGD colleague form, and selecting 'Y' to receive the SGD newsletter.