Little B
URL = http://www.littleb.org/
Description
"The open-source software movement has finally met the world of biological modeling.
Both a language and a program, "little b" gives systems biologists an infrastructure for building and sharing models of cellular activity.
Lacking this, researchers end up making models that nobody else can use, or remaking from scratch what others have already built. That approach works fine for modeling systems like the heart, but grinds to a halt when confronted by thea extraordinary complexity of interlocking molecular datasets.
"You have to be able to break them up into parts and share them," said Jeremy Gunawardena, director of the Harvard Medical School's Virtual Cell Program. "I don't see any other way of confronting the complexity."
He and little b architect Aneil Mallavarapu describe their project in a paper scheduled to be published tomorrow in the Journal of the Royal Society Interface. The paper marks little b's formal debut after five years of development.
During that time, an explosion of gene and protein data -- and a growing appreciation of how subtly and intricately that data is linked -- has fueled the meteoric rise of systems biology, which attempts to describe the networked interaction of genes, proteins and other cellular machinery.
But though they study networked interactions, systems biologists have been, in a sense, isolated: their all-important computer models vary from lab to lab and language to language.
By using little b to describe their work, said Gunawardena, researchers will be able to share information with other researchers. New modules will become available in much the same way as add-ons become available for Firefox -- but instead of customizing a browser, they'll expand a model of cellular function." (http://blog.wired.com/wiredscience/2008/07/open-source-bio.html)