SB Course

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Revision as of 04:24, 30 October 2009 (view source) Igchoi (Talk | contribs) (→2009 Fall) ← Older edit		Revision as of 04:32, 30 October 2009 (view source) Igchoi (Talk | contribs) Newer edit →
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	==Matlab==		==Matlab==
	*Systems biology toolbox		*Systems biology toolbox
		+
		+	==Readings==
		+	*Math tutorials
		+	**[http://neurotheory.columbia.edu/~ken/math-notes/ Ken Miller's Math Notes - UCSF]
	==Term project==		==Term project==

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Revision as of 04:32, 30 October 2009

Contents 1 Biomodel database 2 Running SBML 3 R-project 4 Matlab 5 Readings 6 Term project 6.1 2009 Fall 7 Readings

Biomodel database

• Biomodel DB@EBI
• Simulating Biomodels in JWS online

Running SBML

• SBML softwares - guide table
• KEGG2SBML - KEGG pathway converter to SBML (written in Perl)

R-project

• R package
• BioConductor - based on R package
  • SBMLR package - Manual
  • RSBML

Matlab

• Systems biology toolbox

Readings

• Math tutorials
  • Ken Miller's Math Notes - UCSF

Term project

2009 Fall

• Reconstructing central carbon pathways in target organims
  • Shewanella oneidensis MR-1 KEGG pathway map
    • Lactate metabolism
    • PubMed on flux analysis
  • Saccharophagus degradans 2-40 KEGG pathway map
    • Glucose to Lactate
    • converting KEGG pathway map into 'sbml' by kegg2sbml
    • or using Keggconverter
    • Example
      • glycolysis pathway map - sde0010
      • detailed information (content) - sde0010
      • download pathway map - KEGG ftp

Readings