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NEW: Gepasi 3.0, a metabolic simulator

Pedro Mendes pedro at enzyme.demon.co.uk
Sun Dec 1 13:41:08 EST 1996

This is an announcement of a new major version of the free
biochemical kinetics simulator Gepasi (3.0). Gepasi's home page from
where you can download it (but see also below) is at


Gepasi version 3 is for Windows 95 and Windows NT (3.51 and 
above) only. There are binary versions for Intel and DEC Alpha 

Gepasi is intended for the simulation of the kinetics of systems of
chemical and biochemical reactions. Gepasi is able to simulate the
steady-state and time course behaviour of reactions in several
compartments of different volumes. The user supplies the program
with information about the stoichiometric structure of the pathway,
kinetics of each reaction, volumes of the compartments and initial
concentration of the chemical species. The program then builds the
implicit differential equations and solves them, both for steady
state and time course. Results can be plotted in 2D and 3D graphs
directly from the program (by using gnuplot, included with Gepasi).
Steady states are analysed with metabolic control analysis (MCA) and
linear stability analysis (eigenvalues of the Jacobian). Data is 
output in ASCII columnar files that can easily be loaded in other 

 - improved front-end (merged with simulation engine)
 - runs on Intel and DEC Alpha computers (DEC version to be released)
 - deals with many compartments
 - more kinetic types built-in
 - no limits on number of reactions and metabolites
 - calculation of stability via eigenvalues of Jacobian
 - time-reverse integrations possible (to find unstable steady states)
 - allows for interactive simulations, (perturbations possible)
 - more flexibility in parameter space scans

For more detailed information and to download the package, see 

An earlier version of the program has been described in:
  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.

The program has also been uploaded to the ftp archive at 
bmsdarwin.brookes.ac.uk and soon it will be located at

Pedro Mendes
<pedro at enzyme.demon.co.uk>, (work: <prm at aber.ac.uk>)
author of GEPASI, http://gepasi.dbs.aber.ac.uk/softw/gepasi.html

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