PathwayLab 1.1 Research Edition

Introduction

PathwayLab Research edition is a Mathematica application package designed to analyse, visualise, and document biochemical pathways. The program enables in silico researchers to visualise and document pathways and associated data related to their disease focus.

PathwayLab Research edition has the ability to construct pathway models that can integrate kinetic, gene expression and functional data. This makes PathwayLab Research edition an efficient hypothesis test bench for prediction and analysis of disease pathways, allowing scientists to generate new insights, understand and make better-informed decisions regarding the causes of disorders and potential drug targets.

Computational Analysis & Simulation

Once a pathway model has been specified in PathwayLab Research edition, a number of different methods for analysing 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-catalysed 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 utilised 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 behaviour. PathwayLab Research edition provides an automated mechanism for scanning over ranges of parameter values, in order to find acceptable values of these parameters. Behavioural information (i.e., kinetic formulas, parameters, and mass balances) of implemented pathway models can easily be summarised 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.

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