Overview and Features of SBTOOLBOX2

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
  • 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

Model Representation

Define your models using a simple syntax based on differential equations or based on biochemical reaction equations. To see examples you can click on the figures to the right.

Additionally it is possible to define differential equations, initial conditions, variables, and reactions using a vectorized syntax. An example for which this syntax is useful is:

         d/dt x[n] = kon*x[1]*x[n-1] + koff*x[n+1] - (kon*x[1]+koff)*x[n]

SBML Enabled

The toolbox supports the import and export of SBML models. On this page you can find information about its SBML compatibility.

Experiment Representation

In order to match the in silico implementation to the real workflow in a lab the toolbox allows to describe in silico experiments that are to be performed on the model. Click on the figure to the left to see an example experiment description.

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 the toolbox, visualized, manipulated. Both Excel and comma separated value (CSV) formats are accepted.

Simulation, Analysis, etc.

The toolbox features simulation (both deterministic and stochastic) and a wide range of analysis tools, such as:

Additional Features

Additionally, the toolbox contains many auxiliary functions that are useful for facilitating the access to model or data elements, writing own scripts, and last but not least to make it independent of other commercial MATLAB toolboxes and third party packages.

Documentation

SectionDescription
 
User's Reference Complete user's reference guide. All functions of the toolbox are explained in detail and by examples.
SBML Compatibility Important notes about the compatibility of the toolbox with SBML models.
SBPOP PUBLICATIONS

Publications, discussing results obtained with the help of the SBPOP PACKAGE, are asked to reference the most relevant of the following papers and additionally the link to this webpage:

  • Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515, 2006, doi:10.1093/bioinformatics/bti799
  • SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB, Bioinformatics, 23(5), 646-647, 2007, doi:10.1093/bioinformatics/btl668
  • SBPOP Package: Efficient support for model based drug development from mechanistic models to complex trial simulation, PAGE meeting, Glasgow, UK [abstract]
  • Enhancing population pharmacokinetic modeling efficiency and quality using an integrated workflow, Journal of Pharmacokinetics and Pharmacodynamics, doi:10.1007/s10928-014-9370-4, 2014.
SBPOP NEWS
  • 16th March 2015: Many small improvements ... also SBML export now fully working again
  • 20th January 2015: Many improvements ... Windows 64bit support and compatibility with MATLAB versions >=R2014B
  • 28th July 2014: Happy to announce that our paper about efficient conduct of popPK anlalyses has been published (doi:10.1007/s10928-014-9370-4)
  • 3rd July 2014: Update to Revision 1361 (due to packaging bug in Rev 1352)
  • 18th June 2014: Update to Revision 1352 (popPK modeling workflow MONOLIX and NONMEM, "median" modeling support)
  • 25th March 2014: Update to Revision 1278
  • 7th May 2013: Revision 1172 had a minor bug due to packaging of the public version - main impact on running SBPDgui. Fixed now in Revision 1176
  • 2nd May 2013: SBTOOLBOX2 and SBPD are now integrated into the same package, called "SBPOP PACKAGE". The new combined package additionally includes "SBPOP", focusing on PK/PKPD/PBPK models, population modeling, nonlinear mixed effect parameter estimation, clinical trial simulation