Software

PLAS

PLAS (Power Law Analysis and Simulation) is an interactive, free software program, supporting the dynamical and steady-state analysis of systems of ordinary differential equations (ode's). It was written and is maintained by António Ferreira at the University of Lisbon, Portugal.

While any types of ode's can be analyzed, PLAS's primary applications are GMA and S-system models constructed with power-law functions within Biochemical Systems Theory. PLAS is closed source and does not require programming or compiling. PLAS is featured in the text Computational Analysis of Biochemical Systems. A Practical Guide for Biochemists and Molecular Biologists, xii + 530 pp., Cambridge University Press, Cambridge, U.K., 2000, by E.O. Voit.

Source: www.dqb.fc.ul.pt/docentes/aferreira/plas.html

BSTLab

BSTLab is a free MatLab based toolbox for Biochemical Systems Theory. It was written and is maintained by John Schwacke at the Medical University of South Carolina.

BSTLab is open source and requires familiarity with BST and with MatLab. BSTLab'vs primary applications are GMA and S-system model. The software executes dynamical and steady-state analyses numerically, and, where feasible, symbolically. The latter feature is particularly useful for the method of controlled mathematical comparisons. As such, BSTLab is the supporting software in the paper "Improved Methods for the Mathematically Controlled Comparison of Biochemical Systems." BMC Theoretical Biology and Medical Modelling 1:1, 2004, by J.H. Schwacke and E.O. Voit:

Source: Please contact Dr. John Schwacke

BSTBox

BSTBox is a new software program under development. It was written and is maintained by Gautam Goel at Georgia Tech.

BSTBox supports the entire modeling process within BST and includes the facility to estimate parameter values.

Source: please contact Gautam Goel at gautam.goel@gatech.edu

Gepasi

Gepasi is another software tool for modeling, fitting, and optimizing biochemical systems.

Source: http://www.gepasi.org//

Bestkit

Bestkit is a software tool for web-based analysis, optimization and simulation of biochemical reaction systems.

Source: http://gis.genome.ad.jp/english/result.html/

Cadlive

Cadlive is a web-based software tool for the design, analysis, and simulation of biochemical reaction systems.

Source: http://kurata21.bse.kyutech.ac.jp/cadlive/InputForm.html/