List of software packages that are needed for this course, and those we have decided not to use.

Issues to consider before putting software here: cross platform compatibility, free. Can we find suitable libraries that run on all three platforms (Windows, Mac, and UNIX/Linux flavors).

1. Python (2.5.1) and VPython (download and install both from here)
   • http://www.python.org
   • http://www.vpython.org
   • Download: http://www.vpython.org/download.html
   • Download and install for Windows: Python-2.5.1.msi and VPython-Win-Py2.5-3.2.11.exe
2. numpy: NumPy 1.0.4 (Numerical Python)
   • Documentation: http://www.scipy.org/Tentative_NumPy_Tutorial
   • Download: http://sourceforge.net/projects/numpy
   • Download and install for Windows: numpy-1.0.4.win32-py2.5.exe
3. pylab: PyLab from MatPlotLib (a 2D plotting library)
   • http://matplotlib.sourceforge.net
   • http://matplotlib.sourceforge.net/pylab_commands.html
   • Download: http://sourceforge.net/projects/matplotlib
   • Download and install for Windows: matplotlib-0.90.1.win32-py2.5.exe
   • New version: matplotlib-0.91.2.win32-py2.5.exe (1/6/08)
4. networkx: NetworkX 0.35.1 (for the creation, manipulation, and study of the structure, dynamics, and functions of graphs and networks).
   • https://networkx.lanl.gov/wiki
   • Download: http://cheeseshop.python.org/pypi/networkx/
   • Download and install for Windows: networkx-0.35.1.win32.exe
   • New version: networkx-0.36.win32.exe (pre 1/24/08)
5. Cytoscape: Cytoscape 2.5.1 (for visualizing molecular interaction networks/graphs)
   • http://www.cytoscape.org/
   • download from http://www.cytoscape.org/download.php?file=cyto2_5_1
   • Requires Java SE 5 or Java SE 6

1. numeric: replaced by NumPy and no longer supported
2. snd_util: Python Open AL (correct package site?)
   • http://home.gna.org/oomadness/en/pyopenal/index.html
   • Download: http://download.gna.org/pyopenal/