INDEX

1 - General
2 - Brief description
3 - Installation
4 - Using GNUPLOT with GEPASI

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1 - General

This is GEPASI 2.0, 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,etc. 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
10.

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2 - Brief description

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.

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 is being 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@net.bio.net, post to the list to 
btk-mca@net.bio.net.

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3 - Installation
    
   a) from a disk

      1 - put the installation disk in one drive (for example A:)
      2 - In MS-Windows' Program Manager select File-Run and enter
          A:SETUP.EXE

   b) from the zip file
     
      1 - unzip all files to a disk or directory
      2 - In MS-Windows' Program Manager select File-Run and enter
          A:SETUP.EXE (or the complete path where you've unzipped
          the files to)

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4 - Using GNUPLOT with GEPASI

  To facilitate and speed up the production of plots of the data
generated by GEPASI, this can link to the popular freeware program
GNUPLOT. GNUPLOT has been included in GEPASI's distribution disks.
Otherwise it can be downloaded from network archives and BBSs.

Instructions to install GNUPLOT:

after installing GEPASI, in MS-DOS (it can be a DOS window):

1 - put GEPASI installation disk in a drive (let's suppose it is A:)
2 - in your hard-disk create a directory for GNUPLOT and 'cd' to it
3 - enter the following command: A:WGNPL338
4 - go back to windows and start GEPASI - Simulation
5 - select Plot...
6 - after pressing OK, find the file WGNUPLOT.EXE in the directory
    you've just created, select it and press ENTER
7 - from now on use Plot... to make your plots!

If you obtained GEPASI from a network archive or BBS in a zip file,
you will have to download GNUPLOT separately if you want to install
it with GEPASI (or maybe you already have it...). GNUPLOT for MS-
WINDOWS can be found in the same archives as GEPASI (except the EMBL),
look in directories with the title 'plot' or similar for a file named
wgplt338.zip or something like that (versions previous to version 3.38
have a memory limitation). After downloading it unzip it to a specific
directory and then follow steps 4 to 7 above.


GEPASI 2.0 (c) 1898,1992 by Pedro Mendes.
prm@aber.ac.uk