Team:Illinois-Tools/Resources

From 2009.igem.org

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Revision as of 01:33, 20 October 2009

As a team who relied mostly on technology, we have a unique list of resources that we either used or investigated. The resources that we looked at can be divided into three categories: Software, Journal Articles, and Books

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

Constraint Based Modeling

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

@@ Line 124: / Line 124: @@
 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''''
+====Modules/Libraries====
 * Biopython
 * Networkx