• Python Programming: An Introduction to Computer Science, John Zelle, Franklin, Beedle & Associates, 2004. http://www.fbeedle.com/99-6.html
• Learning Python, M. Lutz, O'Reilly, 2007. http://oreilly.com/catalog/9780596513986/. The electronic version of this text is available through Purdue Libraries at http://proquest.safaribooksonline.com/9780596513986.

• Python Tutorial, Guido van Rossum, Release 2.5.2, 2008; should be in \Python25\Doc; on-line version at http://docs.python.org/tut/
• Think Python: An Introduction to Software Design, Allen B. Downey; http://www.greenteapress.com/thinkpython/thinkpython.html, 2009. Free e-book from Green Tea Press. A more traditional CS intro programming text.

The lab you will be using (LWSN B160) has Windows-based machines. The following software is installed on the machines: Python and VPython, NumPy (Numerical Python), PyLab from MatPlotLib (a 2-D plotting library), NetworkX (for the creation and manipulation of graphs and networks), and Cytoscape (for visualizing molecular interaction networks/graphs). The software is cross platform (Windows, Mac, and UNIX/Linux) and free.

Most students will install this software on their own machine. We have created an install script for installing 1.-4. Download the .zip file from http://www.cs.purdue.edu/~jvalko/secant_pack.zip and unzip the whole archive and run the included install.bat file. This may take a few minutes while to install.

Here are the directions for installing each software individuallu:

1. Python (2.5.2 or 2.5.4) 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
   • Some software packages may have problems with version 2.6 or 3 - 2.5.2 and 2.5.4 are the most stable versions
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