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
  • outputoutput.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 inputs

  • obj – default = random vector with size depending on fbaModel.S
  • printLevel – argument for solveCobraLP function, default = 0

Outputs

  • xx = output.full
  • outputoutput = 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

Output

  • B, L – non-negative basus fi the left nullspace