SB Course

From CSBLwiki

Revision as of 04:22, 30 October 2009 (view source) Igchoi (Talk | contribs) (→2009 Fall) ← Older edit		Revision as of 04:24, 30 October 2009 (view source) Igchoi (Talk | contribs) (→2009 Fall) Newer edit →
Line 27:		Line 27:
	***Glucose to Lactate		***Glucose to Lactate
	***converting KEGG pathway map into 'sbml' by [http://sbml.org/Software/KEGG2SBML kegg2sbml]		***converting KEGG pathway map into 'sbml' by [http://sbml.org/Software/KEGG2SBML kegg2sbml]
		+	***or using [http://www.grissom.gr/keggconverter/DownloadTool.php Keggconverter]
	***<b>Example</b>		***<b>Example</b>
	****glycolysis pathway map - [http://www.genome.jp/kegg-bin/show_pathway?sde00010 sde0010]		****glycolysis pathway map - [http://www.genome.jp/kegg-bin/show_pathway?sde00010 sde0010]

---

Revision as of 04:24, 30 October 2009

Contents 1 Biomodel database 2 Running SBML 3 R-project 4 Matlab 5 Term project 5.1 2009 Fall 6 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

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