Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
Gepasi simplifies the task of model building by assisting the user in translating the language of chemistry (reactions) to mathematics (matrices and differential equations) in a transparent way. This is combined with a set of sophisticated numerical algorithms that assure the results are obtained fast and accurate.
Main Features:
- Gepasi is free software (user license)
- Gepasi runs under Microsoft Windows (95 and above).
- Models in Gepasi v. 3 can be composed of many compartments with different volumes
- The number of reactions and metabolites in each model is only limited by available memory.
- Simulations can be followed interactively (including adding perturbations to a time course)
- Gepasi characterises steady states using Metabolic Control Analysis and linear stability analysis.
- Gepasi's scan utility provides a way for advanced exploration of a model's behaviour in multi-dimensional parameter space
- Gepasi is capable of doing data fitting (parameter estimation) with experimental data.
- Gepasi is capable of finding maxima or minima of any model variables with any number of adjustable model parameters.
- The results of simulations can be plotted in 2D and 3D directly from the program (Gepasi uses the excellent Gnuplot package).
- Gepasi supports SBML level 1 for model interchange with other systems biology modeling software.
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