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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.
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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
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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.
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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!
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