SBMLSim
Laboratorio de Bioinformática y Matemáticas del
Genoma
Universidad de Chile
Santiago, Chile
Introduction
SBMLSim provides a Matlab GUI that allows the user to import a SBML model, simulate it, and visualize the simulations (the SBML model must obviously have specified the kinetic laws that define the system in order to simulate it). The GUI allows to control the numerical parameters of the simulations and allows to easily modify the parameters and initial conditions of the system. It also provides access to the odefile generated from the SBML model in order that the user be able to directly modify it.
The visualization of the simulations consists in the ability to plot any variable or algebraic expression involving the variables and parameters. Multiple plots are also accepted. An interface for defining a base plot is provided, so a complex plot relevant for the system must not be specified each time.
SBMLSim provides a template (specifically built for each system) that allows the user to define a file for computing the equilibrium of the system. This tool uses the Optimization Toolbox of Matlab.
SBMLSim uses the SBMLToolbox for importing the SBML model.
Current Release
The latest release is 1.0.1 beta. This release was tested with Matlab 6.5.0.180913a Release 13 and SBMLToolbox 2.0.1 beta. SBMLToolbox links to libSBML and version 2.3.2 was used in the tests.
Installation
Windows
Download the SBMLToolbox from http://www.sbml.org. Run the installer and when the dialog asks whether to copy the libSBML libraries to the system directory, check that option (you can avoid this step only if you have libSBML previously installed). Then start Matlab, change to the SBMLToolbox/toolbox/ directory (where SBMLToolbox is the directory where you installed the SBMLToolbox), and type 'install' at the Matlab prompt (it's not necessary to exit Matlab after this step). That finishes installing the SBMLToolbox. (It's not necessary to install separately libSBML as, at least for version 2.0.1, the SBMLToolbox installation provides it).
Download the SBMLSim distribution file and unzip it to the directory you choose. That's all.
Linux
libSBML must be installed prior to the rest of the installation. Download the Linux installer from http://www.sbml.org (or directly from SourceForge) and follow the installation instructions. In particular be careful, at the end of the installation, to link the libSBML libraries. In order to do that you must either run 'ldconfig' (these option has been reported not to work) or set the LD_LIBRARY_PATH environment variable to where the libSBML libraries where installed (by default /usr/local/lib). For example, in bash, this is done typing 'setenv LD_LIBRARY_PATH "/usr/local/lib"'. If you use this last option you must either do it each session before running SBMLSim or put the command in an initialization file.
Download the SBMLToolbox distribution file (SBMLToolbox-2.0.1-beta.zip) from http://www.sbml.org (or directly from SourceForge) and follow the Linux installation instructions (available at http://sbml.org/software/sbmltoolbox/).
Download the SBMLSim distribution file and unzip it to the directory you choose. That's all.
Usage
Start Matlab and change to the directory where you unzipped the SBMLSim distribution files. Type 'SBMLSim' at the Matlab prompt and the SBMLSim GUI will show up. Use the menu Model to create a new model or load an existing one.
The distribution files come with anexample, the system 'CellCycle-1997Nov', generated from the SBML model file of the same name, available at http://sbml.org/models/.
Documentation
The distribution comes with a User's Manual (in the docs/ directory) in PDF format.
Author: Daniel Remenik
Date: June 10, 2005