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.

Introducing CodeYear!

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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).

Thursday, November 10th, 10:00 PST/1:00 EST
Registration: http://www.openhelix.com/cgi/webinarInfo.cgi?id=33

There are thousands of bioinformatics and genomics resources that are free and publicly accessible. However, trying to find the right resource for your need, and learn how to use the often complex features and functions can be difficult.

Come explore ways that you can quickly find and effectively learn how to use resources It will include a tour of example resources, organized by categories such as Algorithms and Analysis tools, expression resources, genome browsers (General, Eukaryotic and Prokaryotic/Microbial), Literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation. At the end of the workshop, you’ll learn how to find resources with the OpenHelix free search interface, learning to use resources with OpenHelix tutorials, and a discussion of additional methods of learning about resources.

You’ll learn:

• about several bioscience resources in various subject categories
• to find the right resource using the OpenHelix search interface
• how to quickly learn to use resources through OpenHelix tutorials,
• site documentation, mailing lists, etc.
• about additional resources for discovering resources to meet your research needs

Thursday, November 10th, 10:00 PST/1:00 EST
Registration: http://www.openhelix.com/cgi/webinarInfo.cgi?id=33

Access for Washington University faculty, staff, and students:

Becker Medical Library provides access to the full catalog of tutorials at Open Helix for everyone at Washington University.  Simply register for access using your “wustl.edu” email account at http://www.openhelix.com/cgi/createAccount.cgi.

Graduate Student Awards to Attend the 62nd Annual Meeting of Nobel Laureates and Students in Lindau, Germany, July 1 – July 6, 2012

Internal WU Deadline: 12:00 NOON CST, ON FRIDAY, OCTOBER 28, 2011
Since 1951, Nobel Laureates in chemistry, physics, and physiology/medicine convene annually in Lindau, Germany, to have open and informal meetings with students and young researchers.
The 2012 meeting will be held July 1 – July 6, 2012 and will focus on physics. Meeting details are becoming available (http://www.lindau-nobel.org/WebHome.AxCMS). A list of the Nobel Laureates who will attend the 62nd Meeting will be available when the announcement is made.

The U.S. Department of Energy (DOE) Office of Science, the National Science Foundation (NSF) Directorate for Mathematical and Physical Science Division and Oak Ridge Associated Universities (ORAU http://www.orau.org/ ) are honored to have been invited to bring groups of top young researchers to the 2012 meeting. The U.S. delegation consists of U.S. doctoral students whose current research at their universities is funded by one of the sponsoring agencies (DOE or NSF), Mars, Inc. who sponsors students under separate eligibility criteria or who attend an ORAU member institution. These students will travel to Lindau to participate in discussions with the Nobel Laureates, as well as other graduate students and junior researchers from around the world.

Transportation, lodging and registration expenses are arranged and paid for by the sponsoring agencies. Participants meet in Washington, D.C., for an orientation meeting and travel as a group to Germany. A student awardee will be committed to travel from June 27 or 28, 2012 until July 7 or 8, 2012. The final dates will be determined at a later date.

During the meeting, the Laureates lecture on the topics of their choice related to physics in the mornings and participate in less formal small group discussions with the students in the afternoons and some evenings. In addition to this valuable interaction, the participants enjoy the picturesque island city of Lindau, which is located at the eastern end of Lake Constance, just north of the Swiss Alps. Located at the common border of Austria, Germany, and Switzerland, the medieval city is rich in central European culture (http://www.orau.org/lindau/about/overview.shtml).

The program is administered by the Oak Ridge Institute for Science and Education (ORISE) for DOE and NSF http://orise.orau.gov/.

Washington University has been asked to nominate eight candidates, two for each of the following agencies: DOE, NSF, ORAU, and MARS. Nominees with at least two years of graduate studies and no scheduled PhD defense before December 31, 2012 are eligible. Deadline for submissions is November 15, 2011. A nomination should be initiated by the student’s research mentor to Dr. Kharasch per the directions below. All forms are available at http://www.orau.org/lindau/.

There are four pathways for nominations:

• Department of Energy (DOE): For students who meet the general eligibility criteria and who are sponsored by and/or working on a project, grant, or fellowship sponsored by the U.S. DOE Office of Science (DOE-SC).
• National Science Foundation (NSF): For students who meet the general eligibility criteria and who are sponsored by and/or working on a project, grant, or fellowship sponsored by National Science Foundation Directorate for Mathematical Science Division (NSF-MPS).
• Oak Ridge Associated Universities (ORAU): For students who meet the general eligibility criteria and are attending ORAU member institutions.
• Mars, Inc.: For students who meet the general eligibility criteria regardless of funding source

Eligibility
A student nominated to participate in this program must:

• Be a U.S. citizen;
• Be currently enrolled as a full-time graduate student;
• Be actively involved in a research project. Each sponsor has different requirements. DOE-SC and NSF-MPS require that your research and/or fellowship be funded by their specific offices. ORAU and Mars, Inc. require applicants to be an active researcher who is performing research funded by public or private sources; and
• Have completed by June 2012 at least two years of study toward a doctoral degree in physics or in a related discipline, but not planning a dissertation/thesis defense before December 31, 2012.
• Deadline for submissions is November 15, 2011

A completed nomination consists of:

• a completed nomination form
• a one-page personal resume of the nominee
• a one page letter of reference from the nominee’s advisor and
• an essay of no more than one page written by the nominee describing why participation in the Lindau meeting is important for the nominee’s graduate education.

INTERNAL DEADLINE:

ALL NOMINATIONS MUST BE ELECTRONICALLY SUBMITTED TO DENNETTM@WUSM.WUSTL.EDU BY 12:00 NOON CST, ON FRIDAY, OCTOBER 28, 2011.

Nomination Process:

Application and instructions can be found at http://www.orau.org/lindau/apply/process.shtml

The student’s mentor should transmit the nomination form and other required documents electronically to Evan D. Kharasch, M.D., Ph.D., Vice Chancellor for Research via dennettm@wusm.wustl.edu by 12:00 Noon, Central Standard Time, on Friday, October 28, 2011, for consideration. The institutions’ review panel will review the nominations and choose the 8 candidates to be recommended. The institutions’ nominations are then submitted by the Vice Chancellor for Research (not by the student’s mentor) to the official submission site by 4:00 p.m. EST on Tuesday, November 15, 2011. All components of the application MUST be merged into a single PDF file for upload to the online nomination application. The PDF file cannot be larger than 10 MB.

External Deadline:
All official institutional nomination packages must be submitted by Washington University by 4:00 p.m., Eastern Time, on Tuesday, November 15, 2011.
Notification Date:
Students being recommended to the Council for the Lindau Meeting for this program will be notified by December 31, 2011 using the contact information provided in section B on the nomination form.

This information was authored by Laura Langton – langtonl@msnotes.wustl.edu; corefacilities@msnotes.wustl.edu
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