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Visualizing Markov State Models Using MSMExplorer

A new application automates MSM visualization

An unfolded protein can move through thousands of intermediate structures (conformations) before finding its properly folded state. One approach to understanding this process involves simulating a...
Feb, 19, 2013
New Algorithm Finds Stories in Biomedical Literature

Algorithm joins related publications in a chain from start to finish

A good story ties up all the loose ends. A new data-mining tool takes a stab at doing the same. Dubbed storytelling, the algorithm may make it easier to unearth unexpected connections in the...
Jan, 01, 2007
Extra! Extra! Read All About It

Recent Publications About Biomedical Computing

The field of biomedical computation is increasingly seen as a hot topic worthy of coverage in publications other than Biomedical Computation Review.   In June 2005, The Scientist will publish a...
Jun, 01, 2005
The Last Word
Dear Reader:   Welcome to the first issue of Biomedical Computation Review. With this quarterly publication, we hope to inspire and bring together scientists from the many fields that touch on...
Jun, 01, 2005
Share and Share Alike: A Proposed Set of Guidelines for Both Data and Software
A pair of challenges increasingly threaten the success of bioinformatics research: convincing biologists to share their data and convincing computational colleagues to share their code. Many of us...
Jul, 01, 2006
NCBCs Take Stock and Look Forward: Fruitful Centers Face Sunset

From hardened software to scientific productivity, the NCBCs have changed the landscape for biomedical computing.  What will happen when their funding expires?

It has been eight years since the National Institutes of Health (NIH) funded the first National Centers for Biomedical Computing (NCBCs). With two or three years remaining in the program (...
ccb, i2b2, Magnet, na-mic, ncbo, NCIBI, Simbios
Oct, 19, 2012
Sparks of Hope for a More Open Approach to Scientific Research and Publishing

Transparent peer review, replication studies, and journals of negative results all suggest change is on the horizon

As I was writing this editorial, I learned about yet another scientific paper being retracted. This time it was a genetics paper in Science, one of the hundreds of retractions that the blog...
errors, peer review, replication, scientific publication
Sep, 01, 2011
Error! – What Biomedical Computing Can Learn From Its Mistakes

How errors in data, software, and methodology can teach us how to do better

In 2006, a paper in Nature Medicine suggested a novel and potentially revolutionary method for predicting patient responses to cancer therapies using gene signatures. The finding piqued the interest...
publication, reproducible research, statistics, validation
Sep, 01, 2011
Teaching Resource: Computing Life
Explaining biocomputation to non-scientists can leave a person tongue-tied. Technical jargon gets in the way, and the breadth of the field resists encapsulation.   To help out, and to reach out...
Oct, 01, 2007
Tools to Understand the Federal Research Portfolio: From Ontologies to Topic Mapping

Computation helps evaluate the nature of the NIH research portfolio in ways that were previously very difficult.

What biomedical research does the federal government fund? How is it allocated across important diseases? Has that changed over time? Answering these questions at any level of detail is tougher than...
Jun, 08, 2012
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