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

Chih-Hung Chou; et al. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Institute of Molecular Medicine and Bioengineering, Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China. Nucleic Acids Research, 2009, Vol. 37. April 2009.

Papin, J.A.; et al. Metabolic pathways in the post-genome era. Department of Bioengineering, University of California, San Diego, La Jolla 92093-0412, USA. Trends Biochem Sci. 2003 May;28(5):250-8.

Hintze A, Adami C, 2008 Evolution of Complex Modular Biological Networks. PLoS Comput Biol 4(2): e23. doi:10.1371/journal.pcbi.0040023

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.