Requirements
The following are what we consider the necessary to use PySB as a
biological simulation tool. The versions listed are the ones that are
known to work well with the material in this documentation. Later
versions should work and earlier versions might work. Advanced
users may want to replace these requirements as they see fit.
- Python 2.7: You will need a version of the Python interpreter in your
machine.
- NumPy 1.7: You may not need NumPy for simple model building but you will
want to have it for any sort of numerical manipulation of your
model. The work presented here has been carried out using NumPy 1.7
or later.
- SymPy 0.7: Like NumPy, you may not need SymPy to carry out simple
model building and instantiation but if you want to run numerical
simulation,s SymPy will be a required tool for symbolic math manipulation.
- BioNetGen 2.1.8: The Biological Network Generator is a very useful tool
for rules-based modeling. It is a very powerful and useful package
for modeling and simulation of biological systems and provides a set
of useful tools that could be used with PySB. As of now, PySB uses
BioNetGen as a tool to generate the reaction connectivity network
using its robust engine. If you want to generate biochemical
representations of a biological system, you will need
BioNetGen. BioNetGen depends on Perl 2, so you will need that as
well.
- SciPy 0.10: Scientific Python provides a suite of extremely useful
tools for scientific computing in the Python environment. For
example, SciPy provides the LSODA integrator interface that we use
in PySB.
- MatPlotLib 1.2 (PyLab): This package provides a very useful
interface for generation, manipulation, export, etc of plots in two
and three dimensions. If you want to visualize any type of plots you
will need MatPlotLib.
The easiest way to use PySB
Currently the easiest way to use PySB is through a virtual machine. We
provide an Ubuntu Linux ISO image file based on Ubuntu 12.04
to run PySB. With this you can get acquainted, build some simple
models, and carry out simulations. If you decide you want to use PySB
on your native computer platform we will be posting instructions for
this in the near future.
To run PySB from the image you can download the image from The PySB
website and burn it onto a bootable DVD or USB
stick. Alternatively you can download a virtual machine software such
as Virtual Box (FREE) or Parallels ($). Follow the instructions to setup
the virtual machine booting from the ISO file to begin modeling
with Python programs.