Mathematica and PathwayLab Provide
Computational Systems Biology Environment
August 30, 2005--Wolfram Research, Inc. today began
shipping PathwayLab--an in silico
systems biology software developed by InNetics
AB. This Mathematica application package provides facilities
for modeling, documentation, computational analysis, and information
management of biochemical pathways and networks.
Biochemical pathways and networks are graphical representations of
complex biochemical reaction schemes. These include signaling
pathways, metabolic pathways, and gene regulatory networks. A simple
example of a metabolic pathway is the conversion of glucose into
pyruvate and usable energy.
With PathwayLab, a model of a pathway can be
created using a simple drag-and-drop graphical user interface. The
interface includes graphical building blocks for specifying
biochemical entities as well as reaction and control mechanisms. The
result can be used to document and communicate the model, but more
importantly it is a mathematical model that can be analyzed
computationally. With Mathematica, the pathway model--a system of
coupled nonlinear differential equations--can be directly simulated,
and the simulation result can be further analyzed, including
visualization of the output.
"The PathwayLab-Mathematica combo provides an excellent
systems biology workbench. You can manage the process from modeling
and experimentation to validation," says Roger Germundsson, director
of research and development at Wolfram
Research. "In Mathematica you can leverage the rich
functionality for a wide array of analysis tasks. For instance,
simulating the model with a large number of parameter values is
inherently parallel and can be parallelized using gridMathematica."
Simulating the behavior of a pathway is one important use. But
with Mathematica a whole range of uses opens up, such as model
parameter estimation based on experimental data, steady-state and
stability analysis, and parameter variation in sensitivity and
bifurcation analysis. By analyzing a model, one can effectively do
computer, or in silico, experiments, reducing the need for or guiding
the choice of wet-lab experiments and thus accelerating the process of
drug discovery. "The tight integration between PathwayLab
and Mathematica provides an excellent environment for systems
biology projects," says Mats Jirstrand, co-founder of InNetics and
scientific director of systems biology at Fraunhofer-Chalmers Research
Center for Industrial Mathematics (FCC). "We typically use the
graphical modeling environment provided by PathwayLab for
efficient drag-and-drop pathway construction, initial simulations, and
hypothesis testing, and then use the Mathematica notebook
interface to perform and document the full process from pathway
diagram to advanced computational analysis."
PathwayLab requires Mathematica
and Microsoft Visio and is available for Windows. Trial versions and
more details are available on the Mathematica and PathwayLab websites.
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