Use GEO2R to compare two or more groups of samples in order to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.

A new video on NCBI’s YouTube channel shows how to use GEO2R.

From NIH News:

Rare Disease Day was established to raise public awareness about rare diseases, the challenges encountered by those affected, and the importance of research to develop diagnostics and treatments. There are about 7,000 rare diseases identified in the United States affecting an estimated 25 million Americans. About 80 percent of rare diseases are genetic in origin, and it is estimated that about half of all rare diseases affect children. In addition, what researchers learn by studying rare diseases often adds to the basic understanding of common diseases.

The NIH is hosting Rare Disease Day activities onsite. These activities include recognition of rare disease activities within different agencies and advocacy groups as well as presentations about new technologies.

Suggested Resources:

• Rare Diseases Information from the Office of Rare Diseases Research at NIH
• Wikipedia: Rare Disease Day
• International Rare Disease Day website at http://www.rarediseaseday.org/ and the USA Rare Disease Day website at http://rarediseaseday.us/
• Rare Disease Day on YouTube

Also announced today at NIH is the Genetic Testing Registry (GTR) online tool which will be a useful resource for a variety of people and purposes.

From the press release:

In addition to basic facts, GTR will offer detailed information on analytic validity, which assesses how accurately and reliably the test measures the genetic target; clinical validity, which assesses how consistently and accurately the test detects or predicts the outcome of interest; and information relating to the test’s clinical utility, or how likely the test is to improve patient outcomes.

Video tutorials are available on how to use GTR at GTR Overview and Searching & How to Locate a Genetic Test in Under Three Minutes. You can visit the tool directly at http://www.ncbi.nlm.nih.gov/gtr/.

NCBI now supports IPv6 (beta) for data downloads at http://bit.ly/xiQAsj. More information at  http://1.usa.gov/x655AL .

Please note that NCBI will be taking part in the World IPv6 Launch (http://www.worldipv6launch.org/). On that day (currently anticipated as June 6, 2012), we plan to add IPv6 service to our main FTP Server (http://bit.ly/yerWAX) and shortly thereafter sunset the use of this FTP6 test address (http://bit.ly/xiQAsj).

Team Science Resources

• NIH
  • Collaboration and Team Science
  • Bennett LM, Gadlin H, Levine-Finley S. Collaboration & Team Science: A Field Guide. National Institutes of Health – August 2010 (PDF)
• NIAID
  • Team Science
  • Opportunities and Guidelines to Facilitate Scientific Collaborations
• NCI
  • Team Science Toolkit
• Background information
  • Wikipedia: Science of Team Science
  • PubMed: “team science”[tiab]

There’s even a conference dedicated to team science! The 3rd Annual International Science of Team Science (SciTS) Conference will be held April 16-19 at the Wyndham Chicago. Learn more on the conference website.

Cobo, M., López-Herrera, A., Herrera-Viedma, E. and Herrera, F. (2011), Science mapping software tools: Review, analysis, and cooperative study among tools. Journal of the American Society for Information Science and Technology, 62: 1382–1402. doi: 10.1002/asi.21525

I’m partial to the Network Workbench Tool and Sci² Tool and have used them for various purposes. Both were developed by the Cyberinfrastructure for Network Science Center at Indiana University. Both tools are freely available, both are able to utilize data from diverse sources, and both offer great support materials and tutorials to get you up and running quickly.

This year at Science Online, I have the great pleasure of participating in a session on topics in the area of genomic medicine with Sandra Porter (@digitalbio, of Digital World Biology). Sandy and I have a fun hour planned for everyone – including a skit, real 23andMe data, and some suggestions of online resources (for everyone from researchers and journalists to patients and their physicians)  to learn more about genetics, personalized medicine, diseases, issues, and more.

We are also thrilled to welcome Misha Angrist (@mishaangrist) from the Institute for Genome Sciences & Policy at Duke University to the session where he’ll share his perspectives on this topic during the session. Don’t forget that you can catch Misha Wednesday night at The Regulator Bookshop (720 9th St., Durham, NC) for a reading a book signing of his book, Here Is a Human Being (which is a great read, btw!) .

Session description:

Genomic Medicine: From Bench to Bedside
Saturday January 21, 2012 1:00pm – 2:00pm @ Room 6

I’ll also be chatting about data, the Semantic Web, VIVO and more.  Details about these other sessions are available here. If you can’t attend the meeting, don’t worry – there will be a very active online component.  Follow the meeting at #scio12 on Twitter.

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From the announcement:

NIH LAUNCHES FIRST ONLINE GENETICS COURSE FOR SOCIAL AND BEHAVIORAL SCIENTISTS

A new genetics educational program(http://www.nchpeg.org/bssr/) will provide social and behavioral scientists with sufficient genetics background to allow them to engage effectively in interdisciplinary research with genetics researchers.  The Office of Behavioral and Social Sciences Research (OBSSR) at the National Institutes of Health, partnered with the National Coalition for Health Professional Education in Genetics to create the free, Web-based project.

Increasingly, scientific outcomes are not fully explained by genetic, environmental, or social factors alone or as independent contributors.  Instead, public health advances and scientific breakthroughs tend to rely on transdisciplinary teams of social scientists and genetic researchers.  This creates a greater need among social and behavioral scientists for an understanding of the complexity of the genetic contribution to health, disease and behaviors.

The overarching goal of the course, Genetics and Social Science: Expanding Transdisciplinary Research, is to improve these scientists’ genetics literacy in several key areas, broadly grouped into conversation, imagination, evaluation and integration.  The course will provide sufficient knowledge to support the integration of genetics concepts in the behavioral or social scientist’s own research and will allow for collaborative studies with geneticists. The course will provide users with the ability to conceive of progressive but feasible studies.  Scientists will develop the skills necessary to assess genetics research for validity and utility.

(read more)

NCBI – http://www.ncbi.nlm.nih.gov/

All training and tutorials resources on the NCBI pages are conveniently available on a single page. Some of the most helpful resources have been listed below.  Do take a few minutes to visit the NCBI Education Page, where they provide How-To guides, links to classes and workshops from NCBI, lists of tutorials and problem sets, and tons of great documentation.

The NCBI/NLM YouTube Channel offers some fantastic short videos on everything from BLAST Expect values to the Genome Workbench to using MyNCBI for all sorts of good things.

NHGRI – http://www.genome.gov/

NHGRI collects lecture materials from events and courses and makes them available online – which offers a fantastic way to hear about cutting-edge research topics from the experts in the field. Lectures are often made available on NHGRI’s YouTube channel, www.youtube.com/user/GenomeTV.

A few of the sessions include:

• NHGRI Genomics in Medicine Lecture Series
  BEGINS DECEMBER 2!
• Current Topics in Genome Analysis 2010
  January 12 – March 23, 2010
• Next-Gen 101: Video Tutorial on Conducting Whole-Exome Sequencing Research
  Wednesday, September 28, 2011
• A Decade with the Human Genome Sequence: Charting a Course for Genomic Medicine
  February 11, 2011

…and of course you should check out the fantastic education materials available from NHGRI, too.

1. The BioMart Virtual Issue from Database: The Journal of Biological Databases and Curation (HT @emblebi). If you haven’t had a chance to play with BioMart, please do! From their site:  The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy that promotes collaboration and code reuse.Other publications related to BioMart can be found here and tutorials for BioMart are available from OpenHelix.
2. Its almost time for the annual Database Issue from Nucleic Acid Research (due in January, see the 2011 issue here). Over 100 papers (!!) from the 2012 issue are already available online as Advance Access publications. Of particular note, The UCSC Genome Browser database: extensions and updates 2011 (HT @bffo).