Gepasi  

Biochemical
Simulation

Current version: 3.30
released September 4, 2002

This page last modified: July 30, 2004



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What is Gepasi?

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.

Gepasi is intended primarily for research purposes but because of its user-friendly interface it is equally good for education.

Latest version is 3.30, released on September 2002, added SBML support and other features


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.

Bibliography

A description of the program was published in the journal Cabios:
Mendes, P. (1993) GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Applic. Biosci. 9, 563-571.

and more recently in Trends in Biochemical Sciences (Sept 1997):
Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.

A paper in Bioinformatics describes the application of optimisation methods in bio/chemical modelling with examples carried out in Gepasi:
Mendes, P. & Kell, D.B. (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883.


Who's talking about Gepasi?


Virginia Tech VBI Aberystwyth Quantitative Biology
and Analytical Biotechnology Group

Last modified: July 30, 2004 Copyright © 1996-2004 Pedro Mendes
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