                             Gepasi 3.2
               (Bio)chemical Kinetics Simulation Software

Copyright (C) Pedro Mendes 1989, 1992, 1993, 1996-1998. 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 characterises the steady states that it finds using 
Metabolic Control Analysis and linear kinetic stability analysis. 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 can also use various nonlinear optimisation algorithms 
to search for maxima or minima of any system variable and to fit the 
model parameters to experimental data.

Gepasi 3 was written by Pedro Mendes at the University of Wales
Aberystwyth with funding from the Portuguese JNICT and the UK's BBSRC.


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

Gepasi 3 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 long for any results).


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

Gepasi 3.2 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 3.2 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 gep32xi.zip or gep32xa.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 3.2 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 3.2 as explained above. The two versions will co-
exist as long as they are installed in different directories.

If you have previously installed Gepasi 3.00, 3.01, 3.02, 3.03 or 3.10
you have two options for upgrade:

 - obtain the file "gep320i.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 is an interactive program and its documentation is supplied in
hypertext format as a windows help file. Updates on the documentation
may become 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, July 1998
