Optimalrays¶
- findExtremePathway(fbaModel, obj)[source]¶
Finds an extreme ray
- USAGE
[x, output] = findExtremePathway (fbaModel, obj)
- INPUT
fbaModel – FBA type model
- OPTIONAL INPUT
obj – default = random vector with size depending on fbaModel.S
- OUTPUTS
x – vector from result, where result is an output of solveCobraLP function
output – output.objval contains result.obj
- findExtremePool(fbaModel, obj, printLevel)[source]¶
Finds an extreme ray in the left nullspace of the stoichiometric matrix
- USAGE
[x, output] = findExtremePool (fbaModel, obj, printLevel)
- INPUT
fbaModel – FBA type model
- OPTIONAL INPUT
obj – default = random vector with size depending on fbaModel.S
printLevel – argument for solveCobraLP function, default = 0
- OUTPUTS
x – x = output.full
output – output = solveCobraLP(LPProblem)
- greedyExtremePoolBasis(model)[source]¶
Computes a non-negative basis for the left nullspace of the stoichiometric matrix using optimization to pick random extreme rays, then test a posteriori if each is linearly independent from the existing stored extreme rays.
- USAGE
[B, L] = greedyExtremePoolBasis (model)
- INPUT
model – model structure
- OUTPUTS
B, L – non-negative basus fi the left nullspace