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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 edition of Nature Biotechnology.

The research article, entitled "Automatic generation of cellular reaction networks with Moleculizer 1.0," 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 computational resources.

"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 to develop novel and innovative genomic research projects.

"Moleculizer is exactly the sort of development that one wants to see from multidisciplinary work," explained Dr. Brent. "The mathematical and algorithmic skills that Dr. Lok brought to the problem could only come from one with his strengths, but the work is important because it addresses a problem arising directly from the biology."

Dr. Daniel Gillespie, a pioneer in stochastic methods for modeling chemical kinetics stated, "Dr. Lok has succeeded in adapting and creatively extending earlier developed techniques for stochastically simulating chemical reactions so that they can be used to study real cellular systems, where the huge numbers of potential species and reaction channels makes things very difficult."

Computer simulations can be powerful tools in contemporary molecular biology research, aiding scientists in analyzing data and in testing hypotheses with simulated outcomes before testing them experimentally. The predictive capabilities of computer simulations can also aid biologists in viewing cellular activity over a period of time, by taking advantage of the power of computers to generate the thousands of potential protein complexes and reactions that cells are able to generate.

The Molecular Sciences Institute is an independent nonprofit research laboratory that combines genomic experimentation with computer modeling. Work at MSI aims to weave physics, engineering, computer science, and mathematics together with biology and chemistry to enable precise, quantitative, prediction of the future behaviors of biological systems.

In keeping with the MSI’s support for an open source biology, Moleculizer will be made freely available under the GNU Lesser General Public License.

Nature Biotechnology is "a monthly journal covering the science and business of biotechnology. It publishes new concepts in technology/methodology of relevance to the biological, biomedical, agricultural and environmental sciences as well as covers the commercial, political, ethical, legal, and societal aspects of this research."

Maryanne McCormick | EurekAlert!
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