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Current version: 3.30
released September 4, 2002
This page last modified: September 19, 2002
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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.
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?
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NEW VERSION 3.30 RELEASED ON SEPTEMBER 2002