Gepasi v. 3, simulator of bio/chemical kinetics

Pedro Mendes pedro at enzyme.demon.co.uk
Tue Dec 10 11:55:34 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 see the home page
there you'll find links to download the package from various archives all 
over the world. 

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.

Pedro Mendes                                     Inst. Biological Sciences
prm at aber.ac.uk (home: pedro at enzyme.demon.co.uk)  Univ. Wales, Aberystwyth,
http://gepasi.dbs.aber.ac.uk/pedro/prmhome.htm   Dyfed SY23 3DA, U.K.
http://gepasi.dbs.aber.ac.uk/softw/gepasi.html   FAX: +44 (0)1970 622350

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