SGD Quarterly Newsletter, Summer 2013

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About this newsletter:

This is the Summer 2013 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

YeastMine Upgrade

YeastMine, SGD's powerful search and retrieval tool, has been upgraded to use InterMine version 1.1 software. Highlights of this release include a new format for the template results page, the addition of PantherDB and HomoloGene homology data, an improved representation of Gene Ontology (GO) information, the ability to set background population within the GO enrichment widget, and an option to share lists with other users. In addition to the existing video tutorials, a new Help document describes some common queries. See an overview of these new features in the new video: New, Fun YeastMine 1.1!

What are yeast?

Are you tired of getting asked why you study yeast? And having your grandma’s eyes glaze over when you try to explain your latest research result to her? Well, we here at SGD have decided to help you out. We have revamped our "What are yeast" page to make it even better. We’ve stripped out a lot of the jargon making it much simpler for the nonscientist to read. Not only that, but we’ve consolidated the information onto a single page so you won’t have to link out so much to find what you are looking for.

Community Wiki Updated

SGD's Community Wiki now has a new look and a clearer organization, making it even easier for you to share important information with the yeast community. Use the wiki to record facts about your favorite gene, post a job opening or meeting announcement, or add links to yeast resources. Please contact the SGD help desk for an account that will allow you to log in and add to the wiki.

Sixty New Expression Analysis Datasets

Sixty new datasets have been added to our expression analysis tool at SGD, facilitating the rapid identification of co-expressed genes based on patterns of expression shared with query gene(s) across the entire collection. Expression data are now available at SGD from a comprehensive collection of 430 datasets representing 9190 microarrays from a total of 286 publications. The expression analysis tool can be accessed via the Expression tab and Expression Summary histogram located on Locus Summary pages, or using the 'Expression' option in the Function pulldown in the menu bar at the top of SGD pages. The new data will by default be included with the previous data when using the 'New Search', 'Show Expression Levels', or 'Dataset Listing' options. Alternatively, the new datasets can be specifically filtered using the dataset tag 'not yet curated'. All of the RNA expression data are available for download from the Expression Directory. Datasets are grouped by publication and are in PCL format.

SGD iPhone/iPad App Update

SGD recently updated the "YeastGenome" iPhone, iPad and iPod Touch app to version 1.8.1. Since this version employs a new software method, downloading the newest version of the app is required for continued functionality. The database of yeast gene information within the app has also been updated. The update is available as a free download on iTunes.

Contribute Education Material/Tutorials

SGD is currently developing an "Educational Resources" section for our site. If you are using SGD for classes, lectures or labs, please consider contributing your materials to this shared resource. Selected contributions will also be highlighted in our blog.

Help SGD put the puzzle together

SGD has Locus Summary pages for several hundred genetic loci that aren't mapped to open reading frames. Whenever possible, we would like to connect these loci with the genome sequence. This kind of information is often buried in lab notebooks but never published. Does your lab have information that will let us add a piece to the puzzle? Please contact us if you know of genetic loci that are allelic to physically mapped genes. The list of genetic loci in SGD is available here.

Upcoming Conferences and Meetings

Stara Lesna, Slovakia
June 18 - 22, 2013
Cold Spring Harbor Labs, CSH, NY
July 23 - August 12, 2013
Frankfurt University, Frankfurt, Germany
August 29 - September 3, 2013
Porto Bello Hotel, Antalya, Turkey
September 24 - 28, 2013
Cold Spring Harbor Labs, CSH, NY
November 5 - 9, 2013


*asterisks indicate attendance by SGD

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