- Experiment description functionality (NEW in Ver. 1.8)
- 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
- Determination of the stoichiometric matrix
- Parameter sensitivity analysis
- Network identification
- Parameter estimation
- Determination of moiety conservations
- Simple model reduction
- Bifurcation analysis
- Localization of mechanisms leading to complex behaviors
- Optimization algorithms
- and some specialized functions ...
H. Schmidt, M. Jirstrand: Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics Advance Access, November 2005, DOI 10.1093/bioinformatics/bti799 [PDF]
Tutorial
A tutorial for the toolbox is available now. It can be found here.
Requirements
This toolbox requires at least MATLAB Release 14SP2 (Version >= 7.0.4)
Acknowledgement
This work has been supported by the Swedish Foundation for Strategic Research, which is gratefully acknowledged. It is part of the BIOSIM project, funded by the European Commission.
Documentation License
Copyright (c) 2005-2007, Henning Schmidt, FCCPermission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.2
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the section entitled "GNU
Free Documentation License".
News / History
- 07/05/2007 Version 1.8
- Smaller fixes
- Experiment description, enabling the separation of models and experiments
- 29/01/2007 Version 1.7
- Bug fix in the SBML export and better documentation.
- Minor other bug fixes.
- 24/10/2006
- Improved SBML export. Needed information is determined automatically using SBexportSBML. Additionally a GUI is available that gives the user full control over the SBML export: SBexportSBMLGUI.
- 03/10/2006 Version 1.6
- 18/08/2006
- Added SBML export again (SBexportSBML).
- 24/04/2006
- Added a function SBmca to compute Flux Control Coefficients, Concentration Control Coefficients, and Elasticity Coeffictients.
- 23/03/2006
- Bug fixes in SBexperiment and SBconvert2MA (the latter is needed for SBstochsim.
- 16/02/2006
- Updated documentation (more auxiliary functions are documented now). Type: >> help SBTOOLBOX.
- 10/02/2006
- Simplified installation procedure.
- 20/01/2006
- Bug fix in simplexSB.
- 16/01/2006
- Bug fix in SBexperiment.
- Changed input arguments in fsolveSB. (Options are optional now).
- 10/01/2006
- Adaption to the SBML Toolbox 2.0.2, regarding the time symbol. If the symbol is present all its occurrences will be converted to the time symbol time, used by the Systems Biology Toolbox model representation.
- 08/12/2005
- Bug fix in deleteparametersSB, that lead to an error when running the parameter estimation examples.
- Bug fix in simannealingSB, that lead to a warning and the use of default options when specifying correct options.
- 28/11/2005
- Bug fix in SBsensdatastat.
- 23/11/2005
- The numeric stability of SBsteadystate and SBmoietyconservations has been improved for cases where all states in a model can be described by a stoichiometric matrix and a reaction rate vector.
- 11/11/2005
- The SBparameters function can now return the values of one or more selected parameters.
- 08/11/2005
- Improved syntax checking when converting to TEXTBC model.
- 07/11/2005 Version 1.5
- SBmodels can now be edited and represented in terms of reaction equations, using the function SBeditBC. The previous representation in terms of ODEs is still possible and both representations are interchangeable.
- The function SBcreateTEXTBCfile exports SBmodel into the biochemically oriented text file format.
- Stochastic simulation is now available for SBmodels, using the function SBstochsim (only under Windows). The stochastic simulator is a windows stand alone executable, that can be found at (http://dion.che.udel.edu/multiscale/software.html).
- Import and export functions are considerably faster now, allowing to deal with larger models.
- The syntax for the time/tspan argument in the SBsimulate function has been changed.
- The default integrator has been changed to ode15s.
- The sbmlnotes fields have been taken out of the internal data structure of an SBmodel and have been replaced by the fields type, compartment, and unittype.
- The export of SBML models is disabled in version 1.5. It will be available again in the next version.
- The calling syntax of the SBmodel function has been changed slightly, please read the help text for this function.
- Reactions in SBmodels can now be marked as reversible by setting a flag. In SBedit adding the identifier [reversible] after the kinetic rate expression of a reaction marks it reversible.
- New function SBmakeirreversible, allowing to convert all reversible reactions in an SBmodel into irreversible ones. This requires the ODEs to be specified in reaction rate terms. The reversible reaction rate definitions are required to be defined in the following format: ReactionName = Rforward - Rreverse.
- 13/10/2005
- Bug fixes in SBstoichiometry and SBedit.
- 31/08/2005 Version 1.4
- Functions added that allow to perform parameter estimation. The main function is called SBparameterestimation.
- Local and global optimization method added (simplexSB and simannealingSB). Used for parameter estimation but can be used for other tasks as well.
- Format of the SBdata object has been slightly changed. It is now possible to set a flag for each component in a SBdata object, indicating if this component is measured data or a stimulus that has been applied during an experiment (needed information, e.g., for parameter estimation).
- Functions handling SBdata objects have been changed according to the format changes.
- 30/07/2005
- SBparameters can now also be used to change parameter values of an SBmodel.
- Determination of reaction rates and variable values for given state values possible usnig the functions SBreactions and SBvariables.
- Function SBcreateTempODEfile added, allowing to create the ODE file for an SBmodel and related files in the systems temporary directory.
- 05/07/2005
- Bug fix in the event import of SBML2 models.
- Improvement of the SBstoichiometry function.
- 29/06/2005
- Added the function SBnetworkident to perform network identification based on data from perturbation experiments.
- Bug fix in the import of SBML events.
- Simplified the SBdata object and the format of the Excel and CSV (comma separated value) data files.
- Added the function SBstoichiometry that determines the stoichiometric matrix for a given model. Note that in order to do this the ODEs need to have a certain, but straight forward format, documented in the user's reference guide. When importing a model from SBML the ODEs are already in the required format.
- 03/06/2005 Version 1.3
- Added an SBdata object for the represenation of measurements. Import and export is possible for CSV (comma separated value) and Excel files.
- Added support for state events in the SBmodel description. Events present in SBML models are now imported (read more under Toolbox Documentation/SBML Compatibility), events can be edited using the SBedit function. Functions that can deal with models that contain events are the functions for parameter sensitivity analysis of oscillating systems and, of course, the SBsimulate function. Functions that are not supposed to deal with events will ignore all events in a model and dispay a warning in this case.
- Improvement of the SBedit function. Possibility of updating the model with determined steady-state or last simulation value.
- Fixed an important bug in SBsensdataosc.
- Added SBsensdataoscevents for parameter sensitivity analysis of oscillating systems in the case events are present in the model.
- fsolveSB has been improved (used for solving for the steady-state).
- SBcreateTEXTfile function added.
- SBplot function has been improved.
- SBexperiment function has been added that allows to perform in silico experiments and returns the experiment data as SBdata objects.
- 17/05/2005 Version 1.2
- Major update of the toolbox, where several functions have been improved considerably (especially SBsteadystate, SBmoietyconservations, and the functions for behavior localization).
- Parameter sensitivity analysis has been added.
- A field functionsMATLAB has been added to the data structure of an SBmodel. This field allows to define functions using MATLAB code to be present in the model, which is useful for the implementation of user desired functions, such as a unitstep, etc.
- 15/04/2005
- Added functions SBstates, SBparameters.
- Renamed function SBinitialcondition to SBinitialconditions.
- The function SBmodel can now take a text description of a model (e.g., saved from SBedit) as input argument.
- Bug fix in SBplot, SBreducemodel, and SBlocbehavinteract
- 04/04/2005
- Changed SBcreateODEfile function. The created ODE files allow now to change parameter values of the models they represent.
- 29/03/2005 Version 1.1
- Bug fixes in SBedit, SBsteadystate, SBreducemodel
- Added function to determine moiety conservations (SBmoietyconservations)
- Added functions to localize sources of complex behaviors (SBlocbehavcomp, SBlocbehavinteract)
- Added possibility of saving model as text file from within SBedit. Furthermore, SBedit can be invoked using such a text file description of a model.
- 15/03/2005 Version 1.0