MATLAB Computational Biology Tools

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m
(Systems Biology Toolbox 2)
Line 5: Line 5:
==SimBio Toolbox==
==SimBio Toolbox==
-
==Systems Biology Toolbox==
+
==Systems Biology Toolbox 2==
-
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:
+
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:
-
    * 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
     * Steady-state and stability analysis
-
     * Determination of the stoichiometric matrix
+
     * Stoichiometry
     * Parameter sensitivity analysis
     * Parameter sensitivity analysis
-
    * Network identification
 
-
    * Parameter estimation
 
     * Determination of moiety conservations
     * Determination of moiety conservations
-
    * Simple model reduction
 
     * Bifurcation analysis
     * Bifurcation analysis
     * Localization of mechanisms leading to complex behaviors
     * Localization of mechanisms leading to complex behaviors
-
     * Optimization algorithms
+
     * Statistics (clustering, percentiles, boxplots, etc.)
-
     * and some specialized functions ...  
+
    * Global and local optimization algorithms
-
http://www.sbtoolbox.org/
+
     * 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]]
[[doi:10.1093/bioinformatics/bti799]]

Revision as of 10:06, 21 January 2008

This is the OWW entry page for the MATLAB Computational Biology Tools discussion page (improve these pages with impunity)

Contents

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

General MATLAB Topics

Basic MATLAB user tips

OpenWetWare Resources

Bioinformatics Discussion Group
OWW Computing Resources
Using OpenWetWare

Personal tools