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

All software is free and is cross-platform compatible (running on Windows, Mac,UNIX/Linux ).

1. Python (2.5.2) and VPython not the Visual 5 beta version
   • http://www.python.org
   • http://www.vpython.org
   • Download: http://www.vpython.org/download.html
   • Download and install for Windows: VPython-Win-Py2.5-3.2.11.exe
   • Documentation: http://www.vpython.org/webdoc/visual/index.html
2. NumPy 1.2.1 (Numerical Python)
   • http://numpy.scipy.org/
   • Download: http://sourceforge.net/projects/numpy
   • Download and install for Windows: numpy-1.2.1.win32-py2.5.exe
   • Documentation: http://www.scipy.org/Tentative_NumPy_Tutorial
3. MatPlotLib 0.98.5.2 (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-0.98.5.2.win32-py2.5.exe
   • Tutorial: http://matplotlib.sourceforge.net/users/index.html
4. NetworkX 0.99 (For the creation and manipulation of graphs and networks)
   • https://networkx.lanl.gov/wiki
   • Download: http://cheeseshop.python.org/pypi/networkx/
   • Download and install for Windows: networkx-0.99.win32.exe
   • Tutorial: http://networkx.lanl.gov/tutorial/index.html
5. Cytoscape 2.6.1 (For visualizing molecular interaction networks/graphs)
   • http://www.cytoscape.org/
   • download from http://www.cytoscape.org/download.php?file=cyto2_6_1
   • Requires Java SE 5 or Java SE 6

More specialized, but expected to be used:

1. SciPy 0.7.0b1 - Scientific computations
   • Download: scipy-0.7.0b1-win32-superpack-python2.5.exe
2. GraphViz 2.18 - Graph visualization (needed for PyGraphViz)
   • Download: graphviz-2.18.exe
3. PyGraphViz 0.37: interactive graph visualizations
   • Download: pygraphviz-0.37.win32-py2.5.exe
4. Myro scribbler: software to control scribbler robot.
   • See: Setup
   • This installs Python 2.4 and needed packages. Make sure these install in the right place (C:\Python24) and don't try to overwrite their 2.5 counterparts.
   • Also need the bluetooth software included on the mini-cd with the dongle.

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/