New & Noteworthy
Yeast, More Interesting than your Parents Think
April 23, 2013
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.
So now when your mom asks why you’re wasting your time on yeast, you don’t have to tear your hair out and try to explain it to her. We’ve done the work for you.
You can send her to our reworked page where she can see what makes yeast such an ideal organism to study. She’ll learn that we share a whole lot with yeast even though they are single-celled. Our cells are set up similarly, we share lots of the same genes, and yeast are way easier to grow and manipulate than a person. She’ll see we’ve learned a lot about cancer, Alzheimer’s, Lou Gehrig’s Disease, and so on from our little friends. She’ll learn how useful they are for making existing medicines better and finding new ones. And that’s just a couple of the sections!
After reading this, your friends and family will realize there is much more to yeast than making bread or wine (although these are awesome as well). They will see how useful yeast is for understanding us and they will have a newfound respect for the work you do. At least we hope they will!
Categories: Website changes
Community Wiki Updated
April 22, 2013
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.
Categories: Website changes
SGD Server Move Successfully Completed
December 05, 2012
Thank you for your patience during our move to the new data center last week.
Systems Administrator Stuart Miyasato with the SGD servers in their new location
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.
-Mike Cherry
The new Stanford Data Center housing SGD’s and other servers
Categories: Website changes
SGD Hardware Update
October 09, 2012
We are in the process of migrating SGD servers to new faster hardware! You may have already noticed an increase in performance. There could be some teething issues in the next couple days – so please bear with us!
Categories: Website changes
Expression Data and LiftOver Files Available for Download
February 14, 2012
RNA expression data that are included in SGD’s SPELL expression analysis tool are now available for download in the expression directory. Datasets have been grouped by publication and are 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.
Categories: New Data, Website changes
SGD: New look, new features!
January 26, 2012
SGD has added more than just a new look, we’ve added some great new features!
View the short video “We’ve added more than just a new look…” on Vimeo to learn about our enhanced Search Box and our new navigational menu bar.
Categories: Tutorial, Website changes
Updated Resource: YPL+
January 25, 2012
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.
Categories: New Data, Website changes
Proud to be an SGDer
January 14, 2012
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
Categories: Website changes
SGD Website Updated
January 11, 2012
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.
Categories: Website changes
Filter Expression Data by Experimental Condition
December 16, 2011
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.
Categories: Data updates, Website changes