New & Noteworthy

Happy Holidays from SGD!

December 20, 2016


Happy Holidays from SGD!

We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays.

Stanford University will be closed for two weeks from Wednesday, December 21, 2016 through Tuesday, January 3, 2017. Regular operations will resume on Wednesday, January 4, 2017.

Although SGD staff members will be taking time off, please rest assured that the website will remain up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions.

Happy Holidays and best wishes for all good things in the coming New Year!

Categories: Announcements

Sign Up Now! Next SGD Webinar: December 14, 2016

December 12, 2016


Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, disease associations, alleles and phenotype variants, and functional complementation relationships.

Join our upcoming webinar on December 14th, 9:30 AM PST to learn about homology and disease data in SGD. In this quick 15 minute session, we will demonstrate the best ways to research this information on our website and provide a helpful tutorial on related SGD tools and features. Our webinars are always an excellent opportunity to connect with the SGD team–be sure to bring questions if you have them!

All are welcome to this event. If you are interested attending, please register herehttp://bit.ly/SGDwebinar6

This is the sixth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements, Homologs, Yeast and Human Disease, Tutorial

New SGD Help Video: Finding Human Homology & Disease Information

October 24, 2016


Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, alleles and phenotype variants, functional complementation relationships, and disease associations. There are plenty of ways to find this information on our website, and it takes just 90 seconds to learn how – what are you waiting for?

For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!

Categories: Announcements, Homologs, Yeast and Human Disease, Tutorial

Sign Up Now for the Next SGD Webinar: September 7, 2016

September 02, 2016


The SPELL expression analysis tool at SGD makes it easy to find expression datasets and coexpressed genes that are relevant to your genes of interest. Just plug in a set of genes and go! Once given a query, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and identifies additional genes with similar expression profiles.

Find out how to use SPELL in our upcoming webinar on September 7th, 9:30 AM PDT. This quick 10-minute tutorial will explain how to run a multi-gene query in SPELL, locate expression datasets relevant to your query, and find genes with similar expression profiles.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar5

This is the fifth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements, Tutorial

SGD: New Search, New Style

August 22, 2016


SGD is pleased to introduce our new faceted search, replete with new features that make navigating SGD easier than ever. It’s simple to get started – just click on the “Try this?” button on the SGD homepage. Try a search for your favorite gene or your favorite topic of study in our improved search box! We have also introduced a sleek new look that retains the same familiar features and menus, but is now optimized for mobile use.
 
New features of the search include:
  • Superior search box functionality: New autocomplete options connect to information faster than ever
  • Sorting options: Results sorted alphabetically, by relevance, and by number of annotations
  • Download gene lists: Export gene lists from search results into a text file with the “Wrapped” and “Download” options
  • Faceted searching: Narrow search results by using categories like Genes, Molecular Functions, Phenotypes, and more!
To get familiar with the new search, check out this quick help video to get started:
 

As you explore SGD’s new and improved search, please be sure to send us any feedback via email or through this short survey.
 

Categories: Announcements, Website changes

Coming Soon – New Search and New Styling

August 15, 2016


SGD is planning to release a new faceted search on Monday, August 22, 2016, along with some new site styling optimized for mobile use. The refactored search has been available for the last few months on our beta site: sgd-beta.stanford.edu.

New features of the search include:

  • an expanded selection of fields included in the autocomplete list
  • the ability to enter the SGD site and explore data and pages without an initial query – just click the Explore button and go!
  • narrowing of search results by categories such as genes, molecular functions, and phenotypes (and more!)

Navigating SGD will soon be easier than ever. Please explore the new search, try some different queries, view the new styling on your favorite pages, and send us your feedback via email, or through this short survey.

Categories: Announcements, Website changes

Sign Up Now for the Next SGD Webinar: August 3, 2016

July 28, 2016


SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4

This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements, Tutorial, Sequence

Alliance of Genome Resources – Survey

July 21, 2016


An Alliance of Genome Resources has been formed to provide better support for the biological sciences.

Please help the Alliance by completing the short survey at: http://bit.ly/SGD-AllianceSurvey

Six of the founding members of the Alliance of Genome Resources (Saccharomyces Genome Database, WormBase, FlyBase, ZFIN, MGI, and the Gene Ontology Consortium) attended the GSA’s The Allied Genetics Conference in Orlando from July 13-17. It was a great opportunity for staff of each of these individual resources to talk about their new collaboration to integrate their content and software into a single resource that benefits biologists, educators, and clinicians alike.

The model organism databases all have a long history of reaching out to their respective communities for feedback on new developments and input on future directions. Carrying on this tradition, the Alliance has created a short survey to obtain feedback on how best to provide human disease information in relation to model organisms. In addition, the Alliance is asking for input on the prioritization of website visualizations, tools, and curation of specific data types.

We appreciate your continued support!

Categories: Announcements

Look for SGD at TAGC 2016!

July 05, 2016


SGD staff will be attending The Allied Genetics Conference 2016 (TAGC) on July 13-17, 2016, in Orlando, Florida. We will be hosting a Workshop, Posters, and an Exhibit Booth. We’ll be available during the entire conference to hear your comments or suggestions about SGD and answer your questions.

Five different model organism databases – SGD, WormBase, FlyBase, MGI, and ZFIN – will also be doing open demonstrations and tutorials in the Demo Room (Palms Ballroom Canary 3-4). There will be scheduled group presentations, one-on-one tutorials, troubleshooting and discussions.

Follow @yeastgenome and #TAGC16 on Twitter for the latest research being presented at TAGC.

Workshop: “Getting Even More out of SGD”

Saturday, July 16, 4:00pm – 6:00pm, Crystal Ballroom G2

We’ll be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new genome browser, new data in YeastMine, and more. Bring your questions and comments – we love feedback!

Exhibit Booth

SGD will also have an exhibit booth at the conference, in conjunction with WormBase and FlyBase! Come by booth #530 (right across from the GSA booth) to take a spin on our site, learn about various features of the databases, and provide us with feedback as to what we can do to improve your SGD experience. You might even receive a prize for a good question or suggestion!

…and Psst! Be sure to ask about the newly-formed Alliance of Genome Resources

Posters

In addition to the Workshop, SGD staff will present five posters – please stop by and chat with us.

Poster no. Title Presenter Location Time/Day
Y3076/A The Saccharomyces Genome Database Variant Viewer Olivia Lang Cypress Ballroom 1:30pm – 2:30pm, Thursday, 7/14
Y3168/C Saccharomyces Genome Database: How to find what you are looking for Gail Binkley Cypress Ballroom 1:30pm – 2:30pm, Thursday, 7/14
Y3170/B Saccharomyces Genome Database: Outreach and online training services Kevin MacPherson Cypress Ballroom 1:30pm – 2:30pm, Thursday, 7/14
Y3191/B Integrating Post-Translational Modification Data into the Saccharomyces Genome Database Sage Hellerstedt Cypress Ballroom 2:30pm – 3:30pm, Thursday, 7/14
Y3157/A Homology curation at SGD: budding yeast as a model for eukaryotic biology Stacia Engel Cypress Ballroom 2:30pm – 3:30pm, Thursday, 7/14

Demo Room

SGD, WormBase, FlyBase, MGI, and ZFIN invite all Conference registrants to come to the Demo Room (Palms Ballroom Canary 3-4) to learn how to make the best use of MOD tools and features for your research and teaching.

All day on Thursday 7/14 and Friday 7/15, other than during scheduled group presentations from 12:45pm – 1:30pm and 6:15pm – 7:30pm, personnel are available in the demo room for one-on-one tutorials, troubleshooting and discussions. Make sure you don’t miss the SGD Demo Room presentations on Thursday 7/14 from 6:15pm – 6:30pm and Friday from 12:45pm – 1:00pm!

Find these SGD staff members at the conference:


Mike Cherry
Stacia Engel
Stacia Engel
Pedro Assis
Pedro Assis
Gail Binkley
Gail Binkley
Sage Hellerstedt
Sage Hellerstedt
Kalpana Karra
Kalpana Karra
Olivia Lang
Olivia Lang
Kevin MacPherson
Kevin MacPherson

Categories: Announcements, Conferences

Support Model Organism Databases!

June 22, 2016


Model Organisms such as yeast, worm, fly, fish, and mouse are key drivers of biological research, providing experimental systems that yield insights into human biology and health. Model Organism Databases (MODs) enable researchers all over the world to uncover basic, conserved biological mechanisms relevant to new medical therapies. These discoveries have been recognized by many Nobel Prizes over the last decades.

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While integration presents advantages, the funding cut will cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs.

Leaders of several Model Organism communities, working with the Genetics Society of America (GSA), have come together to write a Statement of Support for the MODs, and to urge the NIH to revise its proposal. We ask all scientists who value the community-specific nature of the MODs to sign this ‘open letter’. The letter, along with all signatures, will be presented to NIH Director Francis Collins at a GSA-organized meeting on July 14, 2016 during The Allied Genetics Conference in Orlando. We urge you to add your name, and to spread the word to all researchers who value the MODs.

In other words, sign this letter!

Categories: Announcements, Yeast and Human Disease, News and Views

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