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