Download and installation

Download

All released versions of the software are available for download on the Sourceforge download page of the project. The latest release is 0.4, published October 15, 2012.

To get the latest developer’s version of the toolbox, you can access the Subversion repository, for example via the command:

svn export http://pybrn.svn.sf.net/svnroot/pybrn/pybrn/trunk pybrn

Software requirements

Required software:

• Python version 2.x with x >= 5.
• NumPy: http://www.numpy.org/

Recommended software:

• libSBML with Python bindings version 3.4.1 or later: http://sbml.org/Software/libSBML required for importing SBML models
• SciPy: http://www.scipy.org required for simulation and steady state computation
• sympy: http://code.google.com/p/sympy/ required for Jacobian computation and for using the Jacobian in numerical computations

Optional software:

• Cython 0.14 or later: http://www.cython.org can be used for efficient network evaluation
• SUNDIALS library 2.3.0 with headers: https://computation.llnl.gov/casc/sundials/main.html can be used in combination with Cython for efficient network simulation

Installation instructions

pybrn is installed via the Python setuptools. For standard installation, simply run the following command in the package’s root directory:

python setup.py install

Depending on your system configuration, you may need administrator rights to do the installation.

Testing the installation

In order to test whether everything works, e.g. all required and recommended packages are available, you can run the following test command before installing the package:

python test/test_all.py

To test the minimal functionality without the need for any of the recommended or optional packages, use the command:

python test/test_minimal.py