New & Noteworthy

Links to S. pombe Orthologs

December 20, 2013

SGD now provides links from individual S. cerevisiae genes to their Schizosaccharomyces pombe orthologs at PomBase. These links are labeled “PomBase”, and can be found on the Locus Summary Pages, within the Homologs section.

Categories: Website changes

More Regulation Data and Redesigned Tab Pages Now Available

November 26, 2013

Transcriptional regulation data are now available on new “Regulation” tab pages for virtually every yeast gene. We are collaborating with the YEASTRACT database to display regulation annotations curated both by SGD and by YEASTRACT on these new pages. Regulation annotations are each derived from a published reference, and include a transcriptional regulator, a target gene, the experimental method used to determine the regulatory relationship, and additional data such as the strain background or experimental conditions. The relationships between regulators and the target gene are also depicted in an interactive Network Visualization diagram. The Regulation tab for DNA-binding transcription factors (TFs) includes these items and additionally contains a Regulation Summary paragraph summarizing the regulatory role of that TF, a table listing its protein domains and motifs, DNA binding site information, a table of its regulatory target genes, and an enrichment of the GO Process terms to which its target genes are annotated (view an example). In the coming months we will be adding this extra information to the Regulation pages of other classes of TFs, such as those that act by binding other TFs.

We have also completely redesigned the web display of the Interactions and Literature tab pages, which now include graphical display of data, sortable tables, interactive visualizations, and more navigation options. These pages provide seamless access to other tools at SGD such as GO tools and YeastMine. Please feel free to explore all of these new features from your favorite Locus Summary page and send us your feedback.

Categories: New Data Website changes

Regulation Information Integrated into SGD

July 18, 2013

The Locus Summary pages of 147 DNA-binding transcription factors (TFs; retrieve the list) now include a new tabbed page, Regulation. This page contains information on the regulatory targets of the TF, its binding sites, and its domains and motifs, as well as a free-text paragraph summarizing its biological context. Take a look at a brief video, below, that explains the different kinds of data found on the Regulation tab. In addition to viewing these data page by page, you can download them all using SGD’s data search and retrieval tool, YeastMine. Click on “Regulation” in the YeastMine menu bar to view the predefined templates for regulation data searches.

 

New Regulation Data at SGD from yeastgenome on Vimeo.

Categories: New Data Website changes

Links to LoQate

July 09, 2013

SGD now provides links to LoQate (the localization and quantitation atlas of the yeast proteome) from the Protein Information section of the Locus Summary Pages. The LoQate database provides localization and abundance data for 5300 yeast proteins at single-cell resolution under three different stress conditions: DTT, H2O2, and nitrogen starvation (Breker et al, 2013, J Cell Biol. 200(6), 839-850). Thanks to Maya Schuldiner for helping us set up the links.

Categories: New Data Website changes

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.

boredom

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.

SGD servers

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

Data Center

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

New Look and Features for Yeast Biochemical Pathways

September 15, 2011

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.

Categories: Website changes

Sequence Data for 26 Additional S. cerevisiae Strains Available

September 06, 2011

SGD has updated both its BLAST Search and Pattern Matching (PatMatch) tools to include genomic, coding, and protein sequences from 26 additional S. cerevisiae strains. Look for more updates and tools from SGD for analyses of the S. cerevisiae strain genomes in the coming months.

Categories: Website changes Sequence

SGD Downloads Site Updated

September 01, 2011

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.

Categories: Website changes

Retiring Advanced Search and Batch Download

August 22, 2011

SGD’s “Advanced Search” and “Batch Download” tools will be retired on August 31st. All of the functions of these tools, plus many more, can be accomplished by YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins.

Short video tutorials that walk you through some of the basic actions in YeastMine are also available.

Categories: Website changes

New Expression Analysis Tool and Datasets

February 23, 2011

Expression analysis at SGD has a new powerful interface and many new datasets. The new interface uses a tool called SPELL (Serial Pattern of Expression Levels Locator). This analysis tool facilitates the rapid identification of the most informative datasets and co-expressed genes based on patterns of expression shared with the query gene(s). By transitioning to this tool, expression data from a comprehensive collection of almost 400 datasets are now available at SGD. The expression analysis tool can be accessed via the expression tab, the expression summary histogram, and in the functional analysis pulldown located on Locus Summary pages. These new data and the SPELL interface have been provided through a collaboration with the SGD Colony at Princeton University. Thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help with data preparation and implementation of SPELL at SGD. SPELL was developed by the Troyanskaya lab at Princeton University (Hibbs et al. (2007) Bioinformatics 23:2692).

Categories: Data updates Website changes

SGD’s Batch Download Tool to be Retired

February 15, 2011

SGD’s Batch Download tool will be retired soon, because all of its functions and many more can now be accomplished via YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins. Please contact us if you have any concerns.

Categories: Website changes

Next