lrs

equivalentSets(model)[source]

Finds the stoichiometrically balanced loops and the equivalent sets

Usage

[loops, eqSets, P, P2, cyclicBool] = equivalentSets(model)

Input

  • model – COBRA Toolbox model with fields:
    • .S - matrix
    • .lb - lower bounds
    • .ub - upper bounds
    • .biomassAbbr - biomass abbreviation

Outputs

  • loops – stoichiometrically balanced loops
  • eqSets – equivalent sets
  • P – as P2 but additinally dependent on cyclicBool
  • P2 – output of lrsOutputReadRay
  • cyclicBool – boolean variable
extremePathways(model, positivity, inequality)[source]

Calculates the extreme pathways of a stoichiometric model using the vertex/facet enumeration package

Usage

[R, V] = extremePathways(model, positivity, inequality)

Input

  • model – COBRA Toolbox model with fields:
    • .description - string used to name files
    • .lb - lower bounds and
    • .ub - upper bounds to derive directionality
    • .b - dxdt

Optional inputs

  • positivity – {0, (1)} if positivity == 1, then positive orthant base
  • inequality – {(0), 1} if inequality == 1, then use two inequalities rather than a single equality

Outputs

  • RnDim by nRay matrix of extreme rays
  • VnDim by nVertex matrix of vertices
extremePools(model, positivity, inequality)[source]

Calculates the extreme pools of a stoichiometric model using the vertex / facet enumeration package

Input

  • model – structure with:
    • .S - m x n Stoichiometric matrix with integer coefficients. If no other inputs are specified it is assumed that all reactions are reversible and S.v = 0
    • .SIntRxnBool - n x 1 boolean vector with 1 for internal reactions
    • .description - description

Optional inputs

  • positivity – {0, (1)} if positivity == 1, then positive orthant base
  • inequality – {(0), 1} if inequality == 1, then use two inequalities rather than a single equaltiy