biotechnology educational software

prm at aber.ac.uk prm at aber.ac.uk
Fri Aug 20 08:09:41 EST 1993


oxford at 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:<MSDOS.BIOLOGY>
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 at aber.ac.uk



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