INDEX 1 - General 2 - Brief description 3 - Installation 4 - Using GNUPLOT with GEPASI ====================================================================== 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 3.0 and 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. ====================================================================== 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 will shortly appear in 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. Alternatively this list can be accessed via the usenet newsgroup bionet.metabolic-reg ====================================================================== 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) ====================================================================== 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. If you obtained GEPASI from an on-line archive or a CD-ROM then you need to get GNUPLOT as well; look in directories named 'windows3' or 'plot'. Instructions to make GEPASI aware of your copy of GNUPLOT (not needed for the diskette version): after installing GNUPLOT, 1 - In GEPASI - Simulation, select Plot... 2 - after pressing OK, find the file WGNUPLOT.EXE in the directory where you've installed GNUPLOT, select it and press ENTER. 3 - from now on use Plot... to make your plots! GEPASI 2.0 (c) 1989,1992,1993 by Pedro Mendes. prm@aber.ac.uk