BioComputational Modeling/Analysis Tools

From BioComputationWiKi

BISEN

The Biochemical Simulation Environment (BISEN) software package is a suite of tools for generating equations and associated computer programs for simulating biochemical systems. BISEN is described in a recent publication. The BISEN page provides links to a user manual with several tutorial examples of increasing complexity that demonstrate its current capabilities, and a download page.

KA Package

This stand-alone package is used for computer-assisted derivation of rate equations for enzymes and transporters. It is based on the schematic methods of King and Altman [57] and uses linear graph theory for generating valid King-Altman directed graphs. The package includes a graphical interface and can output derived rate equations in either MathML or MATLAB format.

• An Introduction to KA Pattern Generator
• KA Pattern Program Download Page
• Feng's slides describing the algorithm are here.

Solution Ionic Composition

• Tool for Calculation A Solution Ionic Composition -- A simple tool for computing free ion concentrations in buffers.