MATLAB Computational Biology Tools

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Bioinformatics Toolbox

SimBio Toolbox

Systems Biology Toolbox

The Systems Biology Toolbox for MATLAB offers systems biologists an open and user extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological systems. It features a wide range of functions:

   * Modeling (based on ODEs and chemical reaction equations)
   * Handling of measurement data
   * Import of SBML models
   * Simulation (deterministic and stochastic)
   * Steady-state and stability analysis
   * Determination of the stoichiometric matrix
   * Parameter sensitivity analysis
   * Network identification
   * Parameter estimation
   * Determination of moiety conservations
   * Simple model reduction
   * Bifurcation analysis
   * Localization of mechanisms leading to complex behaviors
   * Optimization algorithms
   * and some specialized functions ...

http://www.sbtoolbox.org/

doi:10.1093/bioinformatics/bti799