Systems Biology Toolbox 2 for MATLAB
Category Cross-Omics>Pathway Analysis/Tools
Abstract The Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB (see Note 1) is a computational platform for research in Systems Biology.
It offers systems biologists an advanced, 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.
SBTOOLBOX2 features a wide variety of specialized analysis tools and MATLAB adds to that by a large number of built-in functions and a high level scripting language, allowing the user to quickly and efficiently add new functionality.
SBTOOLBOX2 features/capabilities include:
Model Representation --
Define your models using a simple syntax based on differential equations or based on biochemical reaction equations.
Additionally it is possible to define differential equations, initial conditions, variables, and reactions using a vectorized syntax.
Examples for models and their syntax (including the vectorized syntax) can be found in the manufacturer's Model Repository.
SBML Enabled -- SBTOOLBOX2 supports the import and export of Systems Biology Markup Language (SBML) models. Experiment Representation --
In order to match the in silico implementation to the real workflow in a lab SBTOOLBOX2 allows you to describe in silico experiments that are to be performed on the model.
Experiments and models can then be merged to obtain a simulatable model that reflects the defined experiment.
Especially in the case where several different experiments are performed on the same system it is very useful to be able to only keep one copy of the model and to code the different experiments per se.
Measurement Representation --
Measurement data collected during experiments can be imported to SBTOOLBOX2, visualized and manipulated.
Both Excel and comma separated value (CSV) formats are accepted.
Simulation, Analysis, and more --
SBTOOLBOX2 features simulation (both deterministic and stochastic) and a wide range of analysis tools, such as:
- a) Steady-state and stability analysis;
- b) Stoichiometry;
- c) Parameter sensitivity analysis (Local, Global, Customizable metric, Oscillating systems);
- d) Determination of moiety conservations;
- e) Bifurcation analysis;
- f) Localization of mechanisms leading to complex behaviors;
- g) Statistics (clustering, percentiles, box plots, etc.);
- h) Over 15 advanced global and local optimization algorithms;
- i) Representation of models, measurement data, experiment descriptions;
- j) Visualization; Metabolic control analysis;
- k) Signal processing functions; and
- l) Linear and quadratic programming solvers.
Additional Features --
Additionally, SBTOOLBOX2 contains many auxiliary functions that are useful for facilitating the access to model or data elements, writing your own scripts, and last but Not least to make it independent of other commercial MATLAB toolboxes and third party packages.
As an example, it includes an easy to use functionality for building Fortran MEX files under Windows using the MinGW compiler.
SBTOOLBOX2 also allows you to build C/C++ MEX files using the MinGW compiler, leading to a considerable speed-up of the MEX functions compared to the standard MATLAB MEX compiler.
Extensive Documentation --
Tutorials - Collection of comprehensive tutorials for SBTOOLBOX2 and the SBPD extension package (see G6G Abstract Number 20360).
User's Reference - Complete extensive user's reference guide. All functions of SBTOOLBOX2 are explained in detail and by examples.
SBML Compatibility - Important notes about the compatibility of the toolbox with SBML models.
The Systems Biology Toolbox 2 allows you to import Level 1 and 2 SBML models. The export to SBML is only available to generate Level 2 SBML models, etc.
XPPAUT Compatibility - Important notes about the compatibility of SBTOOLBOX2 with XPPAUT - (XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations).
MEX using MinGW - Explains how to build C/C++ and Fortran MEX files on Windows machines using the MinGW compiler and the corresponding functions in SBTOOLBOX2.
Note 1: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and FORTRAN.
System Requirements
Systems Biology Toolbox 2 for MATLAB - Requirements
Manufacturer
- Hening Schmidt
- Fraunhofer-Chalmers Research Centre for Industrial Mathematics
- Gothenburg, Sweden
Manufacturer Web Site Systems Biology Toolbox 2 for MATLAB
Price Contact manufacturer.
G6G Abstract Number 20359
G6G Manufacturer Number 104009