====== Software Packages ======

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



====== Download and Install These Software Packages ======

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

  - **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
  - **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
  - **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
  - **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
  - ** 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:
  - ''SciPy'' 0.7.0b1 - Scientific computations
    * **Download**: [[ http://downloads.sourceforge.net/scipy/scipy-0.7.0b1-win32-superpack-python2.5.exe?modtime=1227623984&big_mirror=0 | scipy-0.7.0b1-win32-superpack-python2.5.exe ]] 
  - ''GraphViz 2.18'' - Graph visualization //(needed for PyGraphViz)//
    * **Download**: [[ http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.18.exe | graphviz-2.18.exe ]]
  - ''PyGraphViz 0.37'': interactive graph visualizations
    * **Download**: [[ http://www.cs.purdue.edu/~jvalko/pygraphviz-0.37.win32-py2.5.exe | pygraphviz-0.37.win32-py2.5.exe ]]
  - ''Myro scribbler'': software to control scribbler robot.
    * **See**: [[ http://wiki.roboteducation.org/Windows_Setup | 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.

====== Software Not Used ======
  - **numeric**: replaced by NumPy and no longer supported 
  - **snd_util**: Python Open AL (//correct package site?//)
    * http://home.gna.org/oomadness/en/pyopenal/index.html
    * **Download**: http://download.gna.org/pyopenal/