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I saw this article on friday and I thought it was very biased. For
example the statement, "It's not a great leap to conceive of a GenBank
for computational models that researchers could contribute to and draw
from." reads as if no such thing currently exists, have they not heard
of SigPath or biomodels.net (which was mentioned in a recent nature
editorial). I know the people in this group and they know full well what
is going on in the community, I think it was just a cheap publicity
stunt to get 'b' marketed. In any case 'b' is not the first of it kind,
there are a number of existing projects which have a similar objective.

Herbert Sauro


_____

From: rphair@integrativebioinformatics.com
[mailto:rphair@integrativebioinformatics.com]
Sent: Sunday, July 10, 2005 1:14 PM
To: 'SBML Discussion List'
Subject: [sbml-discuss] Little b



This is from John Russell's column in Bio-IT World last week.



Two questions: Jeremy, do these high profile systems biologists know
about SBML and the array of solvers that support it? Everyone else, why
LISP?



Harvard Tackles Systems Biology

Towards the end of this summer, Jeremy Gunawardena and Aneil Mallavarapu
of the Virtual Cell Program at Harvard Medical School's Department of
Systems Biology expect to unleash b -- pronounced "little b" -- a new
open-source computer language they hope will energize the biological
modeling community as nothing has before.



Today, a handful of companies and academic groups are building
computational models of disease and biological pathways. To a
considerable extent, these scattered efforts remain in their infancy
(although modeling has recently gained traction inside a few
biopharmas). Moreover, the companies charge for their services and tools
and have a vested interest in controlling their proprietary technology.
On balance, there has been little synergy between these isolated pockets
of progress.



Imagine instead a biologist-friendly language designed specifically to
encapsulate biological knowledge and constantly pounded on and improved
upon by an open-source community. Add to this vision a growing library
of models (and model fragments) written in b and contributed by
researchers worldwide for free use by other researchers. Based on list
processing (LISP), b is designed to be modular, emphasizing the
reusability of modules and a Lego-like approach to model building.



Currently, b focuses on biochemical modeling using ordinary differential
equations. However, Mallavarapu says, "We want to expand to describe
other types of models like partial differential equations, and we're
working on what it will take to write stochastic models."

It's not a great leap to conceive of a GenBank for computational models
that researchers could contribute to and draw from. Imagine the
interesting and productive in silico research that an army of modelers
might undertake.



This is a grand vision for a language with such a diminutive name, and
it is one of the first concrete projects emerging from Harvard's
ambitious foray into systems biology. The department is a little more
than a year old, has enrolled nine students in its Ph.D. program, and
has assembled an impressive faculty led by chair Marc Kirschner, deputy
chair Timothy Mitchison, and Lewis Cantley.



They were "the gang of three who believed sufficiently that something
new was happening to come together and make this [department] happen,"
says Gunawardena, who is the director of the Virtual Cell Program.



Language Barriers

A self-professed "mathematician who fell from grace," Gunawardena had
stints in academia and industry, including a long stay at
Hewlett-Packard doing industrial research. While at HP, he caught the
biology bug and moved to Harvard's Bauer Center for Genomic Research.
That was his first opportunity, he says, "to actually live among
biologists and understand what was going on. Pretty much everything I
thought before I came [to Bauer] turned out to be...modified
substantially." When ideas for the new systems biology department
bubbled up, he was invited to join.



Mallavarapu is a cell biologist and biochemist by training. He took his
Ph.D. with Mitchison at the University of California, San Francisco,
working on photomarking technologies to visualize cytoskeletal dynamics.
During the past few years, Mallavarapu worked at Millennium
Pharmaceuticals developing technology, writing software, and thinking
about what is now b. He credits conversations with Gunawardena for
stoking his desire to make the language a reality, and he recently
joined the Virtual Cell Program as a research scientist. These guys have
great jobs!



Certainly, tricky issues remain. Defining b so that it can be easily
compiled on various LISP platforms isn't trivial. Attracting an early
adopter community will be important. Writing an easy-to-use graphical
user interface is another priority, as is getting models and modeling
techniques published in peer-reviewed literature.



"I think [it's] the classical catch-22 problem: Until there's a
community of people speaking [a language], why would you want to learn
it?" Gunawardena says. "I'm very keen on little b in the context of some
courses that we'll be teaching [and] think that's going to be a very
influential early adopter community. I think it's likely that some of
our colleagues at the medical school and also at MIT are very
interested."



It will be interesting to watch how big little b becomes.