Software

This category includes all programs, libraries, modules, websites, and anything else involving computer technology.

Programming Language

For our web-based program, we used Python 2.5/2.6 programming language in conjunction with the web framework, Django 1.0.2, and MySQL, a relational database management system (RDBMS).

Modules/Libraries

• Biopython
• Networkx
• SciPy
• SoapPy (for KEGG API access)
• Pythongraph
• Pygraphviz (to work with graphviz)
• Pyexcelerator
• Pyopengl
• Matplotlib

Websites

• Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.kegg.jp; our main database that we obtained info from)
• Network Analysis Tools (NeAT; http://rsat.ulb.ac.be/rsat/index_neat.html)

Programs/Other

• Cytoscape (http://www.cytoscape.org/)
• Eclipse
• Graphviz
• Matlab
• COBRA toolbox (for Matlab)

Journal Articles

Becker, Scott; et al.Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.Department of Bioengineering, University of California San Diego.Nature Protocols Vol.2 No.3. March 2007.

• Briefly describes constraint based modeling and give the principles behind it
• Describes the functions of the COBRA toolbox and it explains the output of the program

Price, Nathan; et al. Genome-Scale Models of Microbial Cells: Evaluating the Consequences of Constraints.Department of Bioengineering, University of California San Diego. Nature Reviews. Vol.2. November 2004.

• Describes the constraints one must take into account when creating genome scale models
• Explains each constraint in detail

Books

Lutz, Mark. Learning Python; 2nd ed. Sebastopol, CA: O'Reilly, 2004. Print.

Python cookbook; 2nd ed. Beijing: O'Reilly, 2005. Print.

Minieka, Edward. Optimization algorithms for networks and graphs. New York: M. Dekker, 1978. Print.