Team:Illinois-Tools/Resources

From 2009.igem.org

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*** 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
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=='''Software'''==
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This category includes all programs, libraries, modules, websites, and anything else involving computer technology.
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==Programming Language==
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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).
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==Modules/Libraries==
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* Biopython
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* Networkx
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* SciPy
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* SoapPy (for KEGG API access)
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* Pythongraph
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* Pygraphviz (to work with graphviz)
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* Pyexcelerator
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* Pyopengl
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* Matplotlib
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'''Constraint Based Modeling'''
'''Constraint Based Modeling'''

Revision as of 01:23, 20 October 2009

Researchanimationillinoistools.gif


      • 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