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.