growthExpMatch

growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold, KEGGBlackList)[source]

Runs the growthExpMatch algorithm

Usage

[solution] = growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold, KEGGBlackList)

Inputs

  • model – COBRA model structure
  • KEGGFilename – File name containing Kegg database (.lst file with list of reactions: each listing is reaction name followed by colon followed by the reaction formula)
  • compartment – [c] –> transport from cytoplasm [c] to extracellulat space [e] (default), [p] creates transport from [c] to [p] and from [p] to [c]
  • iterations – Number of iterations to run
  • dictionary – n x 2 cell array of metabolites names for conversion from Kegg ID’s to the compound abbreviations from BiGG database (1st column is compound abb. (non-compartmenalized) and 2nd column is Kegg ID) Both columns are the same length.

Optional inputs

  • logFile – solution is printed in this file (name of reaction added and flux of that particular reaction) (Default = GEMLog.txt)
  • threshold – threshold number for biomass reaction; model is considered to be growing when the flux of the biomass reaction is above threshold. (Default = 0.05)

Output

  • solution – MILP solution that consists of the continuous solution, integer solution, objective value, stat, full solution, and imported reactions

Note

Procedure to run SMILEY:

  1. Obtain all input files (ie. model, CompAbr, and KeggID are from BiGG, KeggList is from Kegg website)
  2. Remove desired reaction from model with removeRxns, or set the model on a particular Carbon or Nitrogen source
  3. Create an SUX Matrix by using the function MatricesSUX = generateSUXMatrix(model, dictionary, KEGGFilename, compartment)
  4. Run it through SMILEY using [solution, b, solInt] = Smiley(MatricesSUX)
  5. solution.importedRxns contains the solutions to all iterations
printSolutionGEM(MatricesSUX, solution, logFile, itNum)[source]

Displays the solution for growthExpMatch iterations

Usage

printSolutionGEM(MatricesSUX, solution, logFile, itNum)

Inputs

  • MatricesSUX – SUX Matrix
  • solution – MILP solution that consists of the continuous solution, integer solution, objective value, stat, full solution, and imported reactions
  • logFile – solution is printed in this file (name of reaction added and flux of that particular reaction) (Default = GEMLog.txt)
  • itNum – number of iterations