SB Course

From CSBLwiki

Contents 1 Biomodel database 2 Running SBML 3 R-project 4 Matlab 5 Readings 6 Term project 6.1 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 package
• BioConductor - based on R package
  • SBMLR package - Manual
    • getIncidenceMatrix (get incidence/stoichiometry matrix from model)
  • RSBML - quick introduction

Matlab

• SimBiology Toolbox provided by Mathworks

M = getstoichmatrix(modelObj)
[M,objSpecies] = getstoichmatrix(modelObj)
[M,objSpecies,objReactions] = getstoichmatrix(modelObj)

• Systems Biology Toolbox 2 - third party toolbox

Readings

• Math tutorials
  • Ken Miller's Math Notes - UCSF
• Metabolic Control Analysis (MCA)
  • Tutorial

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 pathway_gif ftp - The final GIF version of KEGG PATHWAY (to be removed)

library(SBMLR)
library(odesolve)