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:
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.
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.
July 21, 2016
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!
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.
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!
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…
In addition to the Workshop, SGD staff will present five posters – please stop by and chat with us.
|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|
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!
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!
May 26, 2016
If you’re not already using JBrowse to view all your favorite S. cerevisiae genes…you should be! SGD’s JBrowse is a quick and easy way to browse through the information-rich yeast genome. Using JBrowse, you can visualize spatial relationships between genes, locate SGD annotations throughout the yeast genome, and align chromosomal features to hundreds of experimental data sets.
Our upcoming webinar on June 1st will provide a short 15-minute tutorial on the basics of JBrowse. We will demonstrate how to navigate the genome with JBrowse, locate your favorite genes or chromosomal features, and visualize experimental data with data tracks. Whether you’re an experienced GBrowse user looking to try JBrowse for the first time, or someone new to genome browsing as a whole, this webinar is sure to help you get started.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar3
This is the third episode of the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
April 26, 2016
If you’re not already using YeastMine to answer all your questions about S. cerevisiae genes and gene products…you should be! SGD’s YeastMine is a powerful search tool that can retrieve, compare, and analyze data on thousands of genes at a time, greatly reducing the time needed to answer real, practical research questions. Through YeastMine, questions such as “What proportion of plasma membrane proteins are essential?” or “How many different gene products physically interact with the mitochondrial ribosome?” can be answered within minutes.
Next week on May 4th, 2016 at 9:30 AM PDT, we will provide a brief webinar tutorial on how to run queries and create gene lists in SGD’s YeastMine. As a practical demonstration of YeastMine, we will also showcase a research scenario in which yeast-human homology data is used to predict potential chemotherapy targets for human cancers.
Space for this webinar is limited. To reserve your spot, please register for the event using this online form: http://bit.ly/registerFor2ndSGDwebinar
This is the second episode of the SGD Webinar Series. If you missed the first one, or if you’d like to find out more about upcoming webinars, please visit our wiki page: SGD Webinar Series.
March 30, 2016
For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.
The application deadline is April 15th, so don’t miss your chance! Find all the details and application form here.
This year’s instructors – Grant Brown, Maitreya Dunham, and Marc Gartenberg – have designed a course (July 26 – August 15) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:
Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.
Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!
Last year’s Yeast Genetics & Genomics Course was loads of fun – don’t miss out!
January 12, 2016
SGD will be attending The Allied Genetics Conference (TAGC) in Orlando, Florida, July 13–17, 2016! For the first time ever, the meetings of the yeast, C. elegans, ciliate, Drosophila, mouse, and zebrafish model organism communities will be united under one roof, along with a new meeting on population, evolutionary, and quantitative genetics.
Submit your abstracts now! Abstract submission will be open until March 23, 2016. If you want GREAT science and access to the leaders of the field, then TAGC is the place for you. SGD will be there, will you?
December 17, 2015
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 starting at 5:00 p.m. PST on December 18th, reopening on January 4th, 2016. 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.