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

BISEN: Biochemical Simulation Environment

Free PMC article

BISEN: Biochemical Simulation Environment

J Vanlier et al. Bioinformatics. .
Free PMC article


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


Fig. 1.
Fig. 1.
Plots of [ATP], [ADP] and [Mg2+] (A) and pH (B) versus time for the model of ATP hydrolysis of Example 1.

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