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MSI releases 'moleculizer' - a new approach to simulation of intracellular biochemical networks

Dr. Roger Brent, President and Director of Research at the Molecular Sciences Institute ("MSI"), announced today the release of a new approach to simulation of intracellular biochemical networks in the January 2005 edition of Nature Biotechnology. The research article, entitled "Automatic generation of cellular reaction networks with Moleculizer 1.0" (pdf) describes MSI's discrete stochastic event simulator, which keeps track of the thousands of complex species formed from pathway proteins as it simulates reactions between them by a standard Monte Carlo method. A distinguishing aspect of Moleculizer is its ability to generate protein complexes and reactions as they are needed, as opposed to generating all potential complexes and reactions all at once, a task that requires tremendous computer resources beyond the scope of most research labs.

"Moleculizer is a powerful tool that meets a very real need for biologists," explained Dr. Brent. "It is a critical step forward in our quest to provide an accurate simulation of intracellular biochemical networks." "I've designed Moleculizer to be intuitive for biologists," said Dr. Larry Lok, a mathematician who conceived and programmed Moleculizer. "Its parallel simplifications in simulation setup and output provide data in a way that is meaningful and useful to biological researchers." Moleculizer was developed in the context of MSI's "Alpha Project", an ambitious experimental and computational effort to understand the quantitative behavior of a cell signaling pathway in yeast. The Alpha Project is funded by the National Institutes of Health's National Human Genome Research Institute, which designated MSI as a Center of Excellence in Genomic Research. The CEGS program supports multi-investigator, interdisciplinary research teams
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Source:Eurekalert


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