growthExpMatch

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

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)

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