From owner-metabolic-reg@net.bio.net Sat Nov 30 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Pedro Mendes Newsgroups: bionet.metabolic-reg Subject: NEW: Gepasi 3.0, a metabolic simulator Date: 1 Dec 1996 18:41:08 -0000 Organization: Home Lines: 55 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <57sjg4$itb@mserv1.dl.ac.uk> Comments: Authenticated sender is X-mailer: Pegasus Mail for Win32 (v2.42a) MIME-Version: 1.0 Original-To: btk-mca@dl.ac.uk This is an announcement of a new major version of the free biochemical kinetics simulator Gepasi (3.0). Gepasi's home page from where you can download it (but see also below) is at http://gepasi.dbs.aber.ac.uk/softw/gepasi.html Gepasi version 3 is for Windows 95 and Windows NT (3.51 and above) only. There are binary versions for Intel and DEC Alpha computers. DESCRIPTION =========== Gepasi is intended for the simulation of the kinetics of systems of chemical and biochemical reactions. 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 with Gepasi). 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. NEW FEATURES ============ - improved front-end (merged with simulation engine) - runs on Intel and DEC Alpha computers (DEC version to be released) - deals with many compartments - more kinetic types built-in - no limits on number of reactions and metabolites - calculation of stability via eigenvalues of Jacobian - time-reverse integrations possible (to find unstable steady states) - allows for interactive simulations, (perturbations possible) - more flexibility in parameter space scans For more detailed information and to download the package, see http://gepasi.dbs.aber.ac.uk/softw/gepasi.html An earlier version of the program has been described in: Mendes, P. (1993) GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Applic. Biosci. 9, 563-571. The program has also been uploaded to the ftp archive at bmsdarwin.brookes.ac.uk and soon it will be located at ftp://bmsdarwin.brookes.ac.uk/pub/ibmpc/gepasi/Gep300i.zip Pedro Mendes http://www.enzyme.demon.co.uk/pedro.html , (work: ) author of GEPASI, http://gepasi.dbs.aber.ac.uk/softw/gepasi.html .