Bioinformatics@Becker

Updates and Musings from the Bioinformatics team at Becker Medical Library


ScienceOnline & Genomic Medicine

January 18th, 2012 by Kristi

Science Online, held every year in North Carolina, is the the BEST event for experiencing everything related to online science. The conference kicks off tomorrow morning (January 19th) and offers three packed days of sessions, conversations, and fun events! You can learn more about the ScienceOnline in this recent post, ScienceOnline2012 – the Unconference, the Community.

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

Moderators Kristi Holmes, Sandra Porter
This session will serve as an introduction to the topic of personalized medicine from the perspective of major stakeholders including: scientists, physicians, patients and their advocates, community groups and media professionals. We’ll begin with an introduction to the basic concepts and efforts in this area, followed by a discussion of information resources to serve stakeholder groups including relevant clinical, consumer health, and advocacy and policy resources. Various initiatives by government agencies, the commercial sector and academia will be discussed, including: Genetics Home Reference, 23andMe, PatientsLikeMe, and more.

 

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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2012 – the year you learn to code!

January 10th, 2012 by Kristi

If you’re like me, this time of the year always brings about a series of resolutions I set for myself – some serious and some not so much.  Last year I decided that 2012 is the year that I will better develop my coding skills and it appears that the fine folks at CodeAcademy have given us a fabulous way to do just that.

Introducing CodeYear!

Sign up on Code Year to get a new interactive programming lesson sent to you each week and you’ll be building apps and web sites before you know it.

Sign up, learn, and become the hacker you’ve always hoped you could be…


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NIH launches online genetics course

January 3rd, 2012 by Kristi

The new online course presents a nice foundation of information and is targeted to social and behavioral scientists who wish to engage in transdisciplinary collaborations with a genetic component — although the content would be applicable for any number of people who work in complementary areas. The course, Genetics and Social Science: Expanding Transdisciplinary Research, can be found at www.nchpeg.org/bssr.

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)

→ No CommentsCategories:academia, collaboration, education, genetic, Information, NIH, translational

Tutorials and lecture materials from NCBI and NHGRI

November 30th, 2011 by Kristi

I am constantly surprised by the amount of great instructional material available in topics related to genomics and bioinformatics. It is unfortunate that there isn’t a “master list” somewhere of all of the instructional available from NIH-related efforts (hint hint). Until that happens, I’ll try to share resources as I find them. Here are some great resources from the National Center for Biotechnology Information and also from the National Human Genome Research Institute.

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:

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

 

 

→ No CommentsCategories:bioinformatics, BLAST, course, data, database, education, genetic, genome, genomics, informatics, Information, NCBI, NHGRI, research, science, tool, tutorial

Worthwhile reads in bioinformatics…

November 21st, 2011 by Kristi

Just wanted to share some excellent resources in bioinformatics that I happened to catch on Twitter this morning. Both are dedicated issues and both are freely available online (yay!):

  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).

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Webinar: World Tour of Genomics Resources

November 1st, 2011 by Kristi

Webinar:

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.

→ No CommentsCategories:bioinformatics, genomics, helpful, Information, resources, science, software, Washington University, webinar

Graduate Students: Attend the 62nd Annual Meeting of Nobel Laureates and Students in Lindau, Germany

October 24th, 2011 by Kristi

ANNOUNCEMENT from Research News:

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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NIH Office of Extramural Research asks for feedback…

October 20th, 2011 by Kristi

In light of tight budgets and increasing fiscal uncertainty, Dr. Sally Rockey, NIH’s Deputy Director for Extramural Research, asks:

How Do You Think We Should Manage Science in Fiscally Challenging Times?

Dr. Rockey invites readers to take a look at some possible options and supporting data in a set of slides posted on the OER website. Options discussed include: reducing/limiting size of award, limiting the number of awards per PI, limiting the amount of funds per PI, and limiting salaries of PIs.  Do you have input on these options? Ideas for options that are not listed? Feedback is welcome! Comments can be made on Dr. Rockey’s blog or directed to  an email box specifically to receive feedback on these issues, NIHResourceManagement@nih.gov. This is certainly a challenging time for science and this opportunity to learn more (& weigh in!) about steps forward should not be missed.

OEM website: http://grants.nih.gov/grants/oer.htm

→ No CommentsCategories:funding, NIH

Available Now: EpiC Marketplace v0.2 alpha

October 18th, 2011 by Kristi

An announcement from the EpiC Project Team:

The team of the EpiC project at Indiana University is pleased to announce version 0.2 alpha of the EpiC Marketplace (http://epic.cns.iu.edu/).  This version introduces support for sensitive datasets, an overhauled categorization system, and various improvements to security, messaging, search, and design.

What’s New

  • Sensitive datasets can now be registered without publicly sharing the associated files.
  • Updated list of available categories.
  • Datasets, data requests, and projects can now be members of multiple categories.
  • Improvements to the messaging system.
  • Improved security.
  • Improved search performance.
  • Various design improvements.
  • Improvements to registration validation system.
  • Search result views are now paginated.
  • Better default filenames for downloaded dataset archives.
  • Moved from epic.slis.indiana.edu to epic.cns.iu.edu.

Acknowledgments

The EpiC project team is led by Dr. Katy Börner of the School of Library and Information Science, Dr. Steven J. Sherman of Department of Psychological and Brain Sciences, and Dr. Alessandro Vespignani of the School of Informatics.

The EpiC project is supported in part by a National Institutes of Health RM-07-004 award.

http://epic.cns.iu.edu/about/

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YSP has a new website

September 30th, 2011 by Kristi

Be sure to check out the new website for The Young Scientist Program at Washington University School of Medicine.  The site looks great and you can easily find lots of great information, including:

  • more information about the outstanding activities of the group (including their Teaching Teams, Summer Focus, and Teacher/Researcher Partnership programs)
  • what it’s like to be a student or a teacher participating in the program
  • …and most importantly, how to get involved.

Congratulations, YSP team.  :)

 

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