Saturday, July 26, 2008

A Biological Programming Language

I've often said to friends that if I could start my career over again I would go into biology instead of computer science. Now, perhaps, there is a way to have a foot in both worlds.

Little b is a programming language for modeling biological systems. Quoting from the languages site...
The little b project is an effort to provide an open source language which
allows scientists to build mathematical models of complex systems. The
initial focus is systems biology. The goal is to stimulate widespread sharing
and reuse of models. The little b language to allow biologists to build
models quickly and easily from shared parts, and to allow theorists to program
new ways of describing complex systems.

Currently, libraries have been developed for building ODE models of
molecular networks in multi-compartment systems such as cellular epithelia.
Aneil Mallavarapu is the author and inventor of little b, and runs the
project. Little b is based in Common Lisp and contains mechanisms for rule-based
reasoning, symbolic mathematics and object-oriented definitions. The syntax is
designed to be terse and human-readable to facilitate communication. The
environment is both interactive and compilable.

Makes me wonder if Mathematica would be a good enviornment for similar exploration but with more sophisticated tools already built in.

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