                             Gepasi 3.0
               (Bio)chemical Kinetics Simulation Software

Copyright (C) Pedro Mendes 1989, 1992, 1993, 1996, 1997. All Rights Reserved.
Portions of the code are Copyright (C) 1985-1995 Microsoft Corporation. The
associated program "gnuplot" is Copyright (C) 1986-1993 Thomas Williams,
Colin Kelley.

Information in this document is subject to change without notice and does
not represent a commitment on the part of the copyright holder or any other
parties associated with the production of this software and documentation.


INTRODUCTION
============

Gepasi is a Microsoft Windows program intended for the simulation of the
kinetics of systems of chemical and biochemical reactions. The program is
aimed at the study and teaching of the behaviour of such systems. 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 all chemical species. The program then builds the
differential equations that govern the behaviour of the system and solves
them. Results are produced in a flexible way so that data can be imported
into spreadsheets or other data processing programs. The data can also be
plotted in 2D and 3D graphs directly from the program (by using the package
gnuplot that is distributed with Gepasi). Gepasi has the ability of
scanning ranges of values of the system parameters and produce a mapping of
the behaviour of the system within these ranges. Gepasi characterises the
steady states that it finds using Metabolic Control Analysis and linear
kinetic stability analysis.

Gepasi 3.0 was developed by Pedro Mendes at the University of Wales
Aberystwyth under the supervision of Prof. Douglas Kell with funding from
the Chemicals and Pharmaceuticals Directorate of the UK BBSRC.


HARDWARE AND OPERATING SYSTEM REQUIREMENTS
==========================================

Gepasi 3.0 is a Microsoft Windows 32-bit program. It is available in two
versions, one for computers with the Intel 80386 CPU (and above) running
Microsoft Windows 95 and Microsoft Windows NT 3.51 and above; the other is
for DEC Alpha workstations running Windows NT 3.51 and above (not running
unix).

For the Intel version, a Pentium processor is recommended with 8 Mb RAM for
Win95 or 16 Mb for WinNT. For the DEC Alpha version 32 Mb RAM is
recommended. The minimum requirement is an Intel 80386 with 4 Mb RAM (but
be prepared to wait).


AVAILABILITY
============

Gepasi 3.0 is available for download from a series of sites on the 
Internet. The program is also available in CD-ROM software collections and
can be supplied by the author on floppy disks. The primary site for
distribution of Gepasi on the internet is at the URL:

http://gepasi.dbs.aber.ac.uk/softw/gepasi.html

That is where you should look for updates and add-ons for the program.


INSTALATION
===========

The steps you must take to install Gepasi 3.0 depend on how you have
obtained the package. If you have installed a previous version of Gepasi
see the section below (Upgrading).

 - you obtained the file gep30xi.zip or gep30xa.zip from the Internet or
   from a CD-ROM:

    1) unzip the contents of the file onto a temporary directory
    2) run the program setup.exe on that directory and follow the
       instructions

 - you obtained Gepasi 3.0 on floppy disks

    1) insert the floppy disk marked "Disk 1" on a floppy drive
    2) run the program setup.exe on that floppy disk and follow the
       instructions


UPGRADING
=========

If you have previously installed Gepasi 2, there is no path for upgrade,
simply install Gepasi 3 as explained above. The two versions will co-
exist as long as they are installed on different directories.

If you have previously installed Gepasi 3.00, 3.01 or 3.02 you have two 
options for upgrade:

 - obtain the file "gep303i.update.zip" from Gepasi's internet site
   (see above), unzip it to a temporary directory and follow the
   instructions in the file "update.txt"
 
 - uninstall the previous version and then follow the installation
   procedure described in the previous section.
   

DOCUMENTATION
=============

Gepasi 3.0 is an interactive program and its documentation is supplied in
hypertext format as a windows help file. Updates on the documentation are
available on the Internet on the primary site for distribution (see above).
In this package you can find a F.A.Q. file with answers to frequently
asked questions about Gepasi 3.


======================
Aberystyth, March 1997