The Biochemical Simulation Environment (BISEN) software package is a suite of tools for generating equations and associated computer programs for simulating biochemical systems. The Version 1.0.4 package can be used to generate appropriate systems of differential equations for user-specified multicompartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species, and dynamic proton and metal ion buffering.
Software & Databases
Fixed a coding error in IonTempCorr.m which displayed the incorrect initial value for drH (line 91). The error did not affect the overall model. Thanks again to Dr. Michael Cooling!
Corrects an issue with Matlab 2012. A big thanks to Dr. Michael Cooling for his help in finding and correcting this issue!
Dr. Feng Qi has modified and re-written the "BuildDXDT.m" file for better performance.
Dr. Fan Wu and Dr. Kalyan C. Vinnakota modified the "BuildDXDT.m" file of BISEN to explicitly account for water contents and fractional volumes of different compartments. The BSL files are correspondingly formatted to contain these two compartmental properties, as illustraed by examples under the "Examples" sub-folder.The updated BISEN package is released as version 1.0.4. BISEN 1.0.4 is organized to contain 7 sub-folders, in which "BuilderFiles", "Examples", "Databases", and "ExperimentalData" are newly added. Please refer to the User Manual of BISEN 1.0.4 for detailed descriptions.