From owner-metabolic-reg@net.bio.net Thu Aug 19 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!gdt!aber!news From: prm@aber.ac.uk Newsgroups: bionet.software,bionet.general,sci.bio.technology,sci.edu,bionet.metabolic-reg Subject: re: biotechnology educational software Keywords: biotech, education, multimedia, interactive Message-ID: <1993Aug20.130941.19147@aber.ac.uk> Date: 20 Aug 93 13:09:41 GMT References: Sender: news@aber.ac.uk (USENET news service) Reply-To: prm@aber.ac.uk Organization: The University of Wales, Aberystwyth Lines: 81 Xref: biosci bionet.software:5695 bionet.general:5787 sci.bio.technology:567 sci.edu:1456 bionet.metabolic-reg:16 Nntp-Posting-Host: pcfcdh.dbs.aber.ac.uk oxford@cmgm.stanford.edu (Oxford Molecular Ltd.) writes: > >I would be interested in hearing from anyone who has seen or developed any >interactive software for demonstrating concepts and principles of any aspect >of modern molecular biology. I would also be interested in getting feedback >from people on their opinions of such packages, and any views they might >have for developing novel interactive educational software in this field. If you are interested in the dynamics and regulation of metabolic pathways, I have produced an MS-Windows package (GEPASI) just for that. It is freely available from the internet (ftp sites below). DESCRIPTION GEPASI 2.0 is a package for the simulation and modelling of biochemical pathways and chemical reactions. It was made for research but can also be used for educational purposes. With GEPASI you build models of pathways and simulate their dynamics and steady state for given sets of parameters. GEPASI generates the coefficients of Metabolic Control Analysis for steady states. There is also a facility to assist in the study of the effects of several parameters on the properties of the model pathway. GEPASI can be used to simulate systems with stable states, limit cycles and choatic behaviour. There is no manual included but the context-sensitive help includes a short tutorial on metabolic modelling and references to review articles and books about computer simulation in biochemistry, metabolic control analysis, enzyme kinetics and numerical analysis. Also included in the package is the file GEPASI.WRI containing a cut-down version of a paper to appear in "Modern trends in Biothermokinetics", edited by S. Schuster, M. Rigoulet, R. Ouhabi and J.-P. Mazat (Plenum Press) with a short description of GEPASI. A more detailed paper will soon appear in the journal "Computer Applications in the Biosciences". GEPASI runs under MS-WINDOWS 3.1 and is free software, covered by the GNU General Public License. GEPASI uses GNUPLOT (either the DOS or MS-Windows versions), users should download this package and install it to be able to plot the results obtained with GEPASI. A maths co-processor is not necessary but if present will accelerate the simulations by a large factor. GEPASI 2.0 (c) 1989,1992,1993 by Pedro Mendes. AVAILABILITY GEPASI is freely available from the internet as file gep207a.zip from the following FTP sites (site directory). Please chose the closest to your location: EUROPE src.doc.ic.ac.uk /packages/simtel20/biology nic.switch.ch /software/msdos/simtel20/biology ftp.urz.uni-heidelberg.de /pub/simtel/biology ftp.hrz.tu-chemnitz.de /fs12/pub/simtel/msdos/biology swdsrv.edvz.univie.ac.at /pc/dos/biology nic.funet.fi /pub/msdos/SIMTEL20-mirror/biology ftp.vse.cs /pub/msdos/simtel/biology NORTH-AMERICA wsmr.simtel20.army.mil pd1: rigel.acs.oakland.edu /pub/msdos/biology ftp.wustl.edu /systems/ibmpc/msdos/biology ftp.uu.net /systems/ibmpc/msdos/simtel20/biology knot.queensu.ca /wuarchive/systems/ibmpc/msdos/biology cs.ubc.ca /mirror4/msdos/biology AUSTRALIA plaza.aarnet.edu.au /micros/pc/oak/biology SOUTH-AFRICA itu2.sun.ac.za /simtel/biology TAIWAN nctuccca.edu.tw /PC-MsDos/SIMTEL-msdos/biology The subjects of metabolic simulation and metabolic control analysis are discussed in the usenet newsgroup bionet.metabolic-reg. Cheers, Pedro Mendes prm@aber.ac.uk .