KEGG

createUniversalReactionModel(KEGGFilename, KEGGBlackList)

Creates the U matrix using the universal data from the KEGG database

Usage

KEGG = createUniversalReactionModel(KEGGFilename, KEGGBlackList)

Inputs

• KEGGFilename – downloaded from KEGG database (ie. ‘reaction.lst’)
• KEGGBlackList – KEGG reactions not to use

Output

• KEGG – U Matrix

mapKEGGID2Model(model, Dictionary)

This function matches the compound abreviation in model and from CompAbr and connects with the model metabolite the corresponding KEGGID

Usage

model = mapKEGGID2Model(model, Dictionary)

Inputs

• model – COBRA model structure
• Dictionary – consists of:
  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

Output

• model – KEGG model structure

mapMetName2KEGGID(model, Dictionary)

This function maps names of metabolites to KEGG IDs.

Usage

model = mapMetName2KEGGID(model, Dictionary)

Inputs

• model – KEGG model structure
• Dictionary – consists of:
  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

Output

• model – COBRA model structure

transformKEGG2Model(modelKEGG, dictionary)

Translates the metabolites from KEGG to cobra model names.

Usage

model = mapMetName2KEGGID(model, Dictionary)

Inputs

• model – KEGG model structure
• Dictionary – consists of:
  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

Output

• model – COBRA model structure

transformModel2KEGG(model, Dictionary)

Replaces model.mets with model.metKEGGID. If no KEGGID defined, the empty cell will be replaced with metabolite abreviation.

Usage

modelKEGG = transformModel2KEGG(model, Dictionary)

Inputs

• model – COBRA model structure
• Dictionary – consists of:
  • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)
  • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

Output

• modelKEGG – KEGG model structure