SGD Newsletter, August 2016

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About this newsletter:

This is the August 2016 issue of the 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.

Contents

SGD's new Faceted Search Tool

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Explore all the data available at SGD using the facets of our new search!


You may have noticed that SGD has a new look, but the recent changes have not been limited to a website makeover. Introducing SGD's new Faceted Search that allows you to refine your search results by categories! Our developers have been hard at work creating a new search that will not only help you easily find what you are looking for, but also will also allow you to explore more of what SGD has to offer.

If you aren't sure where to start, click the "Try this?" button on the homepage for a random query like "polymerase". From there, you can play around with the various facets to explore all the different types of pages that have to do with "polymerase", like GO term pages, gene pages, reference pages, contig pages, and more!

For more help, check out our video tutorial or contact us. We'd love to hear from you!

Updated Genome Browser (JBrowse)

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Since the last newletter, we have upgraded to JBrowse for our genome browser which improves on the speed of the browser's response and features a search option for data tracks based on author, pmid, topic of the publication and more! To learn about the various features for navigation, searching for data tracks, and uploading data tracks, check out our help videos that can be found through our Youtube channel's playlist on JBrowse!

Keep an eye out for updates on JBrowse as we are looking to regularly add new data tracks. If you have a publication in mind whose data you would like to see incorporated into our genome browser, please send us a message so we can add it to JBrowse!

Three New YeastMine Templates!

Check out our new YeastMine template for retrieving the UTRs (untranslated regions) of a list of genes
We have been getting a lot of user feedback requesting UTR information at SGD recently so in response to your input, SGD has put together a new Gene-->UTR template under the 'Expression' templates in YeastMine! The UTRs are based off transcripts from the Pelachano et al 2013 dataset and the results display information on other datasets that confirm these results.

We've also added two new templates for protein half-life information based on the data from a study by Christiano et al 2014. You can retrieve the half-life information on a list of genes using the Gene-->Protein Half-life template or get a list of genes that have a half-life within a given range by using the Retrieve-->Proteins with half-life in a given range template. Both of these templates can be found in the "Templates" section of YeastMine under the "Protein" category.

Thank you to all who wrote in and be sure to check out the new templates!

Upcoming SGD Webinar: September 7

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The SPELL tool stands for "Serial Pattern of Expression Levels Locator" which helps you search expression datasets at SGD

Exploring Expression Datasets & Coexpressed Genes with SPELL

The next SGD webinar in our Webinar Series is scheduled for September 7th, 2016, 9:30 AM PDT. Ever wonder what that "SPELL" expression tool at SGD does and how you would use it for your research? Have questions about what kind of datasets get added to SPELL and where we get them? This short webinar will provide an overview of how to locate informative expression datasets and coexpressed genes with the SPELL tool that SGD hosts.

To reserve your spot, please register for this event: http://bit.ly/SGDwebinar5

To read about and register for SGD's latest webinars, or to browse the videos and materials of past webinars, visit our SGD Webinars page: SGD Webinars

The ALLIANCE of Genome Resources

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Recently, SGD has teamed up with WormBase, FlyBase, ZFIN, MGI, RGD, and the Gene Ontology Consortium to establish the Alliance of Genome Resources. One of the goals for the Alliance is to provide users (you!) with an integrated approach of accessing the data from all of the Model Organism Databases. This will also provide us with an opportunity to join forces in our tool development efforts to better serve user demand. Read more about the Alliance in the "Genes to Genomes" blog post by the Genetics Society of America.

We are still looking for feedback on input for development and on future directions. Please help us by filling out a short survey for the Alliance.

We’d like to thank everyone that signed the letter to Dr. Francis Collins, Director, NIH. Over 11,000 signatures were collected. The letter and signatures was presented to Dr. Collins just before the TAGC meeting. He responded to the letter during his keynote address at TAGC.

For more updates and announcements on the Alliance, check out the Alliance Facebook page, or check out our twitter page @alliancegenome.

Research Spotlight (Blog Posts)

In case you missed them, here are some of the more popular Research Spotlights posted on our blog lately:

  • Keep Only What You Need At points throughout the Lord of the Rings trilogy, it was necessary for characters to drop all unnecessary baggage for survival. Similarly, yeast keep very few introns, which says something about the introns that stick around, as Hooks and coworkers investigate...
  • Chocolate and Coffee Too In addition to bread and booze, we can thank yeast for their role in processing cacao and coffee. Ludlow and coworkers take a look at the long ignored cacao and coffee strains of yeast and find that they differ greatly from the well-studied wine strains.
  • Can't Get There Like That A new methodology by Rich and coworkers shows that duplication is the only way to boost the expression of SUL1, as opposed to taking the “route” of mutation to the promoter region, under sulfate-limiting conditions.
  • Sometimes Simple is Better In a recent study, Fernandez-Murray and coworkers investigate yeast for the answers to a human condition called congenital sideroblastic anemia caused by a mutation in the human homolog of HEM25.
  • Friends with Benefits Yet another study by Petty and coworkers demonstrates the Awesome Power of Yeast Genetics (#APOYG) using mutants for the gene GCN5, a cancer related gene that is essential in most eukaryotes, but not yeast!

New SGD Help Videos

SGD is actively expanding its library of short video tutorials to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:

Videos are accessible via SGD's YouTube channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to contact us.

SGD at The Allied Genetics Conference (TAGC) 2016 in Orlando FL

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In July 2016, members of the SGD staff attended the The Allied Genetics Conference in Orlando, FL that was organized by the Genetics Society of America. We held a workshop, hosted an exhibit booth, and several of our members presented posters on current SGD projects:

Presenter Poster Title
Stacia Engel Homology Curation at SGD: budding yeast as a model for eukaryotic biology
Gail Binkley Saccharomyces Genome Database: How to find what you are looking for
Olivia Lang The Saccharomyces Genome Database Variant Viewer
Sage Hellerstedt Integrating Post-Translational Modification Data into the Saccharomyces Genome Database
Kevin MacPherson Saccharomyces Genome Database: Outreach and online training services

A big thank you to all of you who stopped by! We are always interested in answering questions and meeting the researchers and users that make up our community. We really appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our both, please feel free to share any comments or suggestions by contacting us!

If you would like to see tweets from the conference, search #TAGC16 on Twitter.

SGD swag: out and about

Do you have pictures to share of SGD swag out and about? Send them to SGD curators for possible inclusion in a future newsletter!

Brenda Andrews represents SGD with her superbud hat in Northwest Territories Canada on the Thelon River
The Yeast Genetics and Genomics class competed with other Cold Spring Harbor courses in a plate race
Showing off that superbud swag at TAGC16 in Orlando! These yeast champs must have completed the crossword puzzle!
Karl Kuchler in Lillooett, British Columbia Canada on the Fraser River with a huge white sturgeon. Why, that's a nice hat you're wearing, Karl!

Recent Publications from SGD Staff

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  1. Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the Saccharomyces cerevisiae reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. PMID: 26989152
  2. Song G, Balakrishnan R, Binkley G, Costanzo M, Dalusag K, Demeter J, Engel SR, Hellerstedt S, Karra K, Hitz B, Nash R, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. PMID: 27252399


What else have we been up to lately?

In addition to The Allied Genetics Conference mentioned above, you may have seen SGD representatives at the following meetings:

  • Senior Biocuration Scientist Stacia Engel and PI Mike Cherry attended the Biocuration 2016 meeting in Geneva, Switzerland in April.
  • Senior Biocuration Scientists Edith Wong and Rob Nash attended the Big Data in Biomedicine meeting at Stanford in May.
  • Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.

Upcoming Meetings

Awaji Yumebutai International Conference Center, Hyogo, Japan
September 11-15, 2016
Abstract submission and early registration deadline: June 10, 2016
EMBL Heidelberg, Germany
October 19 - 23, 2016
Abstract deadline: July 24, 2016
Registration deadline: August 17, 2016
AgroParisTech Claude Bernard campus, Paris, France
May 17-19, 2017
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