Bioinformatics@Becker — Updates and Musings from the Bioinformatics team at Becker Medical Library

Did you know you can just buy lab coats?

February 7th, 2010 by Kristi

Happy Monday everyone, courtesy of XKCD:

(and it is true, you can just buy lab coats)

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Lost in Translation

February 1st, 2010 by Kristi

EMBO Reports published an interesting article today:

Lost in translation

The current focus on translating research into applications might be part of the natural cycle of research funding, but at what cost?

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2010 AMIA Summit on Translational Bioinformatics: late breaking submissions

January 30th, 2010 by Kristi

The 2010 AMIA Summit on Translational Bioinformatics will be held March 10-12 in San Francisco and promises to be a great meeting! AMIA just announced that they are accepting late breaking proposals for paper, panel and poster presentations for the meeting. This is a limited call with a deadline of February 8th, so hurry!

For further information:

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VIVO: Enabling National Networking of Scientists

January 29th, 2010 by Kristi

Last fall, a stimulus award was made by NIH to fund an effort to create a national network of scientists. This award presented an opportunity to create a centralized resource for scientists to discover collaborators and scholarship across institutions. The network is currently comprised of seven institutions: University of Florida, Cornell, Indiana University, Washington University in St. Louis, Scripps Research Institute, Weill Cornell Medical College, and Ponce Medical College. VIVO is an open source, semantic web platform and data include HR data, grants, publications, and more. The project is a major step toward making the research enterprise more efficient.

You might be thinking to yourself, “Why not just use Facebook or LinkedIn to find collaborators?” Social networking platforms such as Facebook, LinkedIn, and others are great resources – I use them myself. Unfortunately, these platforms aren’t designed to offer many of the features that a national network of scientists needs to succeed:

VIVO is populated with information from authoritative sources (such as institutional databases and national grants and publications databases). Other platforms depend on users to input all to profile information – and the information may or may not accurately reflect the individual’s true identity.
VIVO integrates data and provides it in a consistent format which is readable and interoperable by not just humans, but machines too.
VIVO uses standard ontologies & controlled vocabularies, making it easy to find what you’re looking for – whether it is a collaborator, an event, or more.

The VIVO Collaboration institutions have been busy over the past few months with development, national outreach activities, local implementation of VIVO platforms, and the final touches on the project website. Stay tuned for updates!

For more information:

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Bioinformatics Workshops at WUSM

January 27th, 2010 by Kristi

Becker Medical Library will be offering a series of lunchtime bioinformatics workshops every Monday beginning February 1, 2010. Classes will introduce a range of topics (see schedule, below). Major databases and software tools will be discussed.

LOCATION: Room 601B, Becker Medical Library
TIME: 12:00 noon
REGISTRATION: No registration is required, seats will be available on a first-come, first-served basis.

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PubMed updates

January 26th, 2010 by Kristi

There are some great updates planned for PubMed in February:

A link to an updated and enhanced Limits page will be available on all pages
The homepage will include a link to the clipboard
The Advanced search page will be updated

Pediatric cancer genome project

January 25th, 2010 by Kristi

Washington University School of Medicine and St. Jude Children’s Hospital have teamed up on a $65 million project to sequence the genomes of 600 pediatric cancer patients.

Read more at MassGenomics and the St. Louis Business Journal

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Developing bioinformatics programming skills…

January 24th, 2010 by Kristi

Take some time to read A Quick Guide for Developing Effective Bioinformatics Programming Skills by Joel Dudley and Atul Butte. The paper was published last month in PLoS Computational Biology and judging from the PLoS article-level metrics, it is being put to good use!

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2010 AMIA Summit on Translational Bioinformatics

January 17th, 2010 by Kristi

Registration is open for this year’s AMIA Summit on Translational Bioinformatics. The Summit will be held February 10-12, 2010 at the Parc 55 Hotel, San Francisco, California. The meeting promises a great program with interesting submission topics and loads of informative tutorials:

(T01) Introduction to Translational Bioinformatics
Atul Butte, Stanford University
(T02) An Introduction to Clinical Natural Language Processing
Leonard D’Avolio, VA Boston Healthcare System; Wendy Chapman, University of Pittsburgh; Dina Demner-Fushman, National Library of Medicine; John Pestian, Cincinnati Children’s Hospital
(T03) Ontologies in Biomedicine
Mark Musen, Stanford University and the National Center for Biomedical Ontology
(T04) A Primer on i2b2
Description to come.

Read about last year’s Summit here and here and check out the AMIA Summit on Clinical Research Informatics held March 12-13, 2010 also held at the Parc 55.

Hope to see you there!

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