Software Tools

Based on the network stoichiometry and sign constraints imposed on the boundary fluxes, this Matlab-based package is used to predict thermodynamically feasible reaction directions.

BELUGA is a MATLAB optimization package implementing a genetic algorithm based on PIKAIA. BELUGA finds a constrained local minimum x of an objective function given an initial population of candidate solutions.

This web based bio-thermodynamic database can be used to obtain formation properties and dissociation constants (provided as pK’s) for reference species associated with biochemical reactants at specified temperature and ionic strength and to obtain reaction properties (including free energies and enthalpies) for associated reactions.

The BISEN software package is a suite of tools for generating equations and associated computer programs for simulating biochemical systems.

A toolbox for causally cohesive genotype-phenotype studies.

JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data.

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 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.

A Matlab-based suite of tools for building models of microvascular transport and exchange from 3D structural information.

MATLAB code for the NP-complete exhaustive calculation of the minimal cycle basis (MCB) for a biochemical network is given here. A MATLAB script demonstrating calculation of the MCB for a few example networks is also included.

OpenCOR is an open source cross-platform modelling environment for creating and using CellML encoded models.

A software tool for annotating biosimulation models with rich semantics and composing models in a modular, automated fashion.

A Matlab-based suite of tools for calculation of the free cation in physiological buffer.

A MATLAB tool for the specification, construction, and exact reduction of state transition system models of biochemical processes.