MATLAB Computational Biology Tools

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Bioinformatics Toolbox

SimBio Toolbox

Systems Biology Toolbox 2

The Systems Biology Toolbox 2 for MATLAB offers systems biologists a powerful, open, and user extensible environment, in which to build models of biological systems. Experiments can be performed on models, just like in real lab life but in silico. The representation of models, experiments, and measurement data is intuitive and easy to use. The toolbox features a wide variety of specialized analysis tools and MATLAB adds to that by a large number of inbuilt functions and a high level scripting language, allowing the user to quickly and efficiently add new functionality. Inbuild simulation and analysis tools include:

   * Steady-state and stability analysis
   * Stoichiometry
   * Parameter sensitivity analysis
   * Determination of moiety conservations
   * Bifurcation analysis
   * Localization of mechanisms leading to complex behaviors
   * Statistics (clustering, percentiles, boxplots, etc.)
   * Global and local optimization algorithms
   * etc.

The SBPD extension package for the Systems Biology Toolbox 2 adds high-speed simulations, combination of models, experiments, and measurement data in so called projects. Functions are available that support the complete model building process (modeling, simulation, identifiability analysis, model reduction, parameter estimation (multiple experiment and multiple measurement fitting), validation, etc.). The projects are a powerful construct that allows to keep a perfect overview over your modeling task at any time. Graphical user interfaces support the workflow.

http://www.sbtoolbox2.org/

doi:10.1093/bioinformatics/bti799