Installation Guide

Please follow the procedures below to install the Systems Biology Toolbox for MATLAB and eventual additional needed software on your computer.

Installation of the Systems Biology Toolbox

Windows & UNIX

Unzip the SBTOOLBOX.zip file to the desired location of the toolbox. Start MATLAB and change into the folder SBTOOLBOX.
Execute installSB.
Now you can use the toolbox.

If you want to be able to import/export SBML models / perform bifurcation analysis you need to install the SBMLToolbox / XPPAUT before installing the Systems Biology Toolbox.

Installation of the SBMLToolbox

Download the desired package of the SBMLToolbox, and follow the installation instructions included in the downloaded package.
Then you need to add the root directory of the SBML Toolbox and all its subdirectories to the MATLAB path. You can do this manually in MATLAB or by editing the path information in the installSB.m file, by setting the variable PATH_SBMLTOOLBOX.
Please use always the newest version of the SBML Toolbox.

Installation of XPPAUT

Windows

Download and unzip the file to the root folder of "C:".
Open xpp.bat and remove the pause command in the last line.
Add the root directory of the XPPAUT installation to the MATLAB path. You can do this either manually, or by editing the path information in the installSB.m file, by setting the variable PATH_XPPAUT.
In order to run XPPAUT on Windows an X-Server is required. Please refer to the XPPAUT page for more information about that. Please note that there is a pure Windows version of XPPAUT, but you should use the X version!

UNIX

Unpack and untar the file to a temporary location.
Type make to compile the program.
Move the executable xppaut to the desired location.
Add the directory in which the xppaut executable is located to the MATLAB path. You can do this either manually, or by editing the path information in the installSB.m file, by setting the variable PATH_XPPAUT.

Installation of the Stochastic Simulator

Windows Download the file stochastic_sim.exe and place it in the folder SBTOOLBOX/stochsim.

UNIX Not available for UNIX/Linux

SBTOOLBOX Addons

Other Links

Installation Guide

Installation of the Systems Biology Toolbox
Windows & UNIX	Unzip the SBTOOLBOX.zip file to the desired location of the toolbox. Start MATLAB and change into the folder SBTOOLBOX. Execute installSB. Now you can use the toolbox. If you want to be able to import/export SBML models / perform bifurcation analysis you need to install the SBMLToolbox / XPPAUT before installing the Systems Biology Toolbox.

Installation of the SBMLToolbox
Download the desired package of the SBMLToolbox, and follow the installation instructions included in the downloaded package. Then you need to add the root directory of the SBML Toolbox and all its subdirectories to the MATLAB path. You can do this manually in MATLAB or by editing the path information in the installSB.m file, by setting the variable PATH_SBMLTOOLBOX. Please use always the newest version of the SBML Toolbox.

Installation of XPPAUT
Windows	Download and unzip the file to the root folder of "C:". Open xpp.bat and remove the pause command in the last line. Add the root directory of the XPPAUT installation to the MATLAB path. You can do this either manually, or by editing the path information in the installSB.m file, by setting the variable PATH_XPPAUT. In order to run XPPAUT on Windows an X-Server is required. Please refer to the XPPAUT page for more information about that. Please note that there is a pure Windows version of XPPAUT, but you should use the X version!
UNIX	Unpack and untar the file to a temporary location. Type make to compile the program. Move the executable xppaut to the desired location. Add the directory in which the xppaut executable is located to the MATLAB path. You can do this either manually, or by editing the path information in the installSB.m file, by setting the variable PATH_XPPAUT.

Installation of the Stochastic Simulator
Windows	Download the file stochastic_sim.exe and place it in the folder SBTOOLBOX/stochsim.
UNIX	Not available for UNIX/Linux