A new version of Gepasi is now available for download from its home page:
(follow the "download" link).
Gepasi is a Windows 95/NT program for the simulation of the kinetics of
chemical and biochemical 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
the chemical species. The program then builds the implicit differential
equations and solves them, both for steady state and time course. Results
can be plotted in 2D and 3D graphs directly from the program (by using
gnuplot, included here). Steady states are analysed with metabolic control
analysis (MCA) and linear stability analysis (eigenvalues of the
Jacobian). Data is output in ASCII columnar files that can easily be
loaded in other programs.
- Command line version of Gepasi (bgepasi.exe) to execute a series of
simulations. Useful to set up batches and scheduled simulations.
- New predefined kinetic types: reversible Hill kinetics.
- Gepasi now attempts to determine the "branch structure" of the pathway.
- Other front-end enhancements.
- Intel version now catches overflows and divisions by zero.
- Scaling of elasticities towards external metabolites.
- Other minor bugs fixed
Gepasi is Freeware.
Pedro Mendes Inst. Biological Sciences
prm at aber.ac.uk (home: pedro at enzyme.demon.co.uk) Univ. Wales, Aberystwyth,
http://gepasi.dbs.aber.ac.uk/pedro/prmhome.htm Ceredigion SY23 3DA, U.K.
Author of Gepasi, biochemical kinetics simulator