GEPASI - WIN 3.1 simulator of metabolic pathways
prm at aber.ac.uk
prm at aber.ac.uk
Tue Mar 23 14:43:55 EST 1993
GEPASI is a general purpose simulator of metabolic pathways.
It is a directed towards research and education; it is meant to be a
very useful tool for modelling biochemical pathways, chemical
reactions, and other dynamic systems. GEPASI is free software
covered by the GNU general public license, version 1.
This version of GEPASI runs under MS-Windows 3.1 in 386 enhanced mode,
on 80386SX and above microprocessors. A maths co-processor is not
needed but should accelerate the simulations by at least a factor of
In order to simulate bichemical pathways, the user must first define
the reactions that are part of the pathway, all its parameters and
initial concentrations of the metabolites (chemical species). GEPASI
then determines the dynamics and steady state (if there is one),
including the coefficients defined in Metabolic Control Analysis.
GEPASI can be used to study metabolic regulation, chemical and enzyme
kinetics including oscillatory (limit cycle) and chaotic reactions.
To be able to produce plots of the simulated data from within the
program, you must have the (excellent) freeware graphics program
GNUPLOT. You can find the windows version of GNUPLOT in the same
archives as GEPASI (see below) in a directories named 'plot' (instead
The file GEPASI.WRI contains a cut-down version of a paper to appear
in "Modern trends in Biothermokinetics", edited by J.-P. Mazat, S.
Schuster and M. Rigoulet and published by Plenum Press with a short
description of GEPASI. Another more detailed paper has been submitted
to the journal "Computer Applications in the Biosciences".
For more detailed information see the help file (GEPASI.HLP). The
subjects of metabolic simulation and metabolic control analysis are
discussed in the mailing list btk-mca. To subscribe to this list send
a mail message to biosci at net.bio.net, post to the list to
btk-mca at net.bio.net.
GEPASI can be retrieved by anonymous FTP from the following archives:
UK src.doc.ic.ac.uk packages/ibmpc/simtel20/biology/gep205b.zip
USA wsmr-simtel20.army.mil <MSDOS.BIOLOGY>gep205b.zip
USA oak.oakland.edu pub/msdos/biology/gep205b.zip
AUS archie.au micros/pc/oak/biology/gep205b.zip
FIN nic.funet.fi pub/msdos/SIMTEL20-mirror/biology/gep205b.zip
please use the archive closer to you!
GEPASI is also available from the EMBL email server but the version there
archived is older than that in the archives above. Also the brave, can try
anonymous FTP to 126.96.36.199 (my own pc) where you will find the newest
version of GEPASI in the directory gepasi/gep206a.zip. This version will be
uploaded to the other FTP archives in the near future (note that this
server only accepts one FTP request at a time and is not foolproof; use it
only between 19.00 and 10.00 GMT).
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