Journal Article

BISEN: Biochemical Simulation Environment

J. Vanlier, F. Wu, F. Qi, K. C. Vinnakota, Y. Han, R. K. Dash, F. Yang and D. A. Beard

in Bioinformatics

Volume 25, issue 6, pages 836-837
Published in print March 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI:
BISEN: Biochemical Simulation Environment

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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


Journal Article.  1023 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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