BISEN: Biochemical Simulation Environment

Bioinformatics. 2009 Mar 15;25(6):836-7. doi: 10.1093/bioinformatics/btp069. Epub 2009 Feb 25.


Summary: The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering.

Availability: The software and a user manual (including several tutorial examples) are available at

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Biochemical Phenomena*
  • Computational Biology / methods*
  • Software*