lrs

• lrsInterface

equivalentSets(model)

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)

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

• R – nDim by nRay matrix of extreme rays
• V – nDim by nVertex matrix of vertices

extremePools(model, positivity, inequality)

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