GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems

Abstract

GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows. For any system of up to 45 metabolites and 45 reactions, each with any user-defined or one of 35 predefined rate equations, one can produce trajectories of the metabolite concentrations and obtain a steady state (if it does exist). When steady-state solutions are produced, elasticity and control coefficients, as defined in metabolic control analysis, are calculated. GEPASI also allows the automatic generation of a sequence of simulations with different combinations of parameter values, effectively scanning a hyper-solid in parameter space. Together with the ability to produce user-defined columnar data files, these features allow for both very quick and systematic study of biochemical pathway models. The source code (in C) is available on request from the author, and while the user interface is dependent on having MS-Windows as the operating system, the numerical part is portable to other operating systems. GEPASI is suitable both for research and educational purposes. Although GEPASI was written with biochemical pathways in mind, it can equally be used to stimulate other dynamical systems.