Systems Biology Toolbox 2 for MATLAB

64bit Windows Version of SBTOOLBOX2/SBPD

The 64bit Windows version is now available (see download and installation section).

The Systems Biology Toolbox 2 (SBTOOLBOX2) 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.

Main Features SBTOOLBOX2

Representation of models, measurement data, experiment descriptions
SBML import/export
Deterministic and stochastic simulation
Visualization
Steady-state and stability analysis
Metabolic control analysis
Stoichiometric analysis
Parameter sensitivity analysis (Local, Global, Customizable metric, Oscillating systems)
Determination of moiety conservations
Bifurcation analysis
Localization of mechanisms leading to complex behaviors
Statistical functions
Signal processing functions
Over 15 powerful global and local optimization algorithms
Linear and quadratic programming solvers

The SBPD extension package (SBPD) 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.

Main Features SBPD

Combining models, experiments, and measurement data to projects
Automatic generation of C-code simulation models, resulting in 30-200 x faster simulation than MATLAB integrators
Parameter estimation (multiple experiment, multiple measurement)
Parameter fit analysis
Analysis of residuals
Identifiability analysis
Model reduction
37 preinstalled kinetic rate laws
Dynamic sensitivity analysis (Parameters, Initial conditions)
Manual tuning of model parameters
Intuitive and powerful GUIs
SBPD can easily be used by users who have no programming knowledge!

People who are publishing scientific results obtained with the help of the SBTOOLBOX2 and SBPD are asked to reference the following paper and url:

Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515, 2006. (www.sbtoolbox2.org). [BibTeX]

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