Dear Colleagues,
I'm pleased to announce the release of a new version of Gepasi,
the biochemical kinetics simulator. Gepasi 3.30 is available for
FREE download at http://www.gepasi.org .
New features in Gepasi 3.30:
- SBML import/export (SBML is an XML format intended to share
models between different software programs)
- 3 new optimization algorithms (simulated annealing, praxis,
and Nelder & Mead)
- The support program MEG is now included in the installation
of Gepasi. MEG is for creating models of repeated units, such
as cell cultures.
- minor improvements on the user-interface
- several bug fixes (including a bug in calculations involving
non-unitary volumes)
Gepasi is intended for the simulation of chemical and biochemical
reactions. Gepasi is able to simulate the steady-state and time
course behavior 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.
Steady states are analysed with metabolic control analysis (MCA) and
linear stability analysis (eigenvalues of the Jacobian). Gepasi can
further fit parameters to experimental data and carry out
optimisation of any model variable. Data is output in ASCII columnar
files that can easily be loaded in other programs.
More information about Gepasi and downloads from http://www.gepasi.org
Pedro Mendes
http://www.vbi.vt.edu/~mendes
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