SB Course

From CSBLwiki

Contents 1 Biomodel database 2 Running SBML 3 R-project 4 Term project 4.1 2009 Fall

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

Term project

2009 Fall

• Reconstructing central carbon pathways in target organims
  • Shewanella oneidensis MR-1 KEGG pathway map
    • Lactate metabolism
  • Saccharophagus degradans 2-40 KEGG pathway map
    • Glucose to Lactate