PathwayLab 1.1 Research Edition

Modeling and Simulation Tool for Biochemical Networks

PathwayLab Research Edition is a Mathematica application package designed to analyze, visualize, and document biochemical pathways. PathwayLab Research Edition permits in silico researchers to visualize and document pathways and associated data related to their disease focus. The ability to construct pathway models that can integrate kinetic, gene expression, and functional data makes PathwayLab Research Edition an efficient hypothesis test bench for prediction and analysis of disease pathways. This allows scientists to better understand, generate new insights on, and make better-informed decisions regarding the causes of disorders and potential drug targets.

"The understanding of the roles of our targets in the context of biological pathways are central to target validation. We have a clear need for a tool for building and sharing hypotheses of these pathways.... We believe InNetics' technology and engineering competence represents a strong platform for the development of this tool. We're very pleased to be able to work with them." Martin Norin, Director, Structural Chemistry, Biovitrum AB

Computational Analysis & Simulation
Once a pathway model has been specified in PathwayLab Research Edition, a number of different methods for analyzing the model can be applied. In a steady-state analysis, the set of concentrations for a model's biochemical entities can be computed in a way that corresponds to constant concentrations and reaction rates. A transient analysis, on the other hand, computes how the concentrations and flows of the entities in the pathway change dynamically over time.

PathwayLab Research Edition also supports metabolic control analysis (MCA) for systematic studies of how the enzyme-catalyzed steps in a pathway or network of pathways influence a particular reaction rate. MCA provides a ranking of the enzymes with respect to their relative influence. Hence, the pathway models can be utilized to study and interpret what a change in activity of potential targets for drug development actually represents in a wider biological system context.

Parameter settings of a pathway model often have a significant impact on its behavior. PathwayLab Research Edition provides an automated mechanism for scanning over ranges of parameter values, in order to find acceptable values of these parameters. Behavioral information (i.e., kinetic formulas, parameters, and mass balances) of implemented pathway models can easily be summarized using the PathwayLab Research Edition report generator. In addition, the complete set of equations and parameters of a model can be exported for use in Mathematica.

The package comes with electronic documentation, which is fully integrated in the software.

PathwayLab Research Edition is developed and supported by InNetics AB.

InNetics AB
Teknikringen 7
SE-583 30 Linköping
Sweden
phone: +46-(0)13-211880
fax: +46-(0)13-211880
email: info@innetics.com
technical support: support@innetics.com
web: http://innetics.com/mathematica

PathwayLab 1.1 Research Edition requires Mathematica 4.0 or higher and Microsoft Visio 2002 or 2003 and is available for Windows 2000/XP.