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