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info needed re met.simulation SCAMP

Pedro Mendes prm at aber.ac.uk
Tue Sep 6 09:16:53 EST 1994


Patrick G Swann <swannp at delphi.com> writes:

>I'm looking for a program to simulate product yields from multi-sequence
>(possibly branching) pathways given initial substrates and kinetic constants. 
>I' ve heard that SCAMP can do this and am interested in any information 
>regarding availability.  Many Thanks.

SCAMP is available by ftp from

ftp://bmsdarwin.brookes.ac.uk/pub/software/atari/scamp/scamp25g.zip

or

ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/scamp/scamp25g.zip

Alternatively if you want to use MS-Windows, you can use GEPASI, available 
from the same site:

ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/gepasi/gep208c.zip

with the source code in

ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/gepasi/gsrc208c.zip

below is a short description of GEPASI:

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 in "Modern trends
in Biothermokinetics" (1993), edited by S. Schuster, M. Rigoulet, R.
Ouhabi and J.-P. Mazat (Plenum Press) with a short description of
GEPASI. 

A more detailed paper on GEPASI has been published in journal "Computer
Applications in the Biosciences". The full reference is: 

Mendes P., (1993) GEPASI: a software package for modelling the dynamics,
steady states and control of biochemical and other systems. Comput. Appl.
Biosci. 9, 563-571.


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.

NOTE: 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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