Systems Biology on the Grid

Courtesy of CellwareThere are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms

Sam Jaffe
Jul 4, 2004
<p></p>

Courtesy of Cellware

There are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.

That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms, while in metabolic expression reactions, stochastic algorithms work better," says Dhar. "We couldn't find anything that integrated the different algorithms into the same software package, so we built our own."

Cellware's Java-based client resembles a Web browser and runs under Windows, Mac OS, or Linux. The back-end computational engine, written in C++, can be used on a grid, a first for a systems biology-modeling program. Thus, a model can be created anywhere in the world, exported in SBML (Systems Biology Markup Language), and run...