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)

INPUTS

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 INPUT

  • 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, param)[source]

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

INPUT

model.S - `m x (n + k)

OPTIONAL INPUTS

  • model.SConsistentRxnBool – n x 1 boolean indicating stoichiometrically consistent metabolites

  • model.SIntRxnBool - Boolean of reactions heuristically though to be mass balanced.

  • model.SIntMetBool - Boolean of metabolites heuristically though to be involved in mass balanced reactions.

  • 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

OUTPUT

  • P – p x m matrix of non-negative entries such that P*N = 0.

  • vertexBool n x 1 Boolean vector indicating which columns of P are vertices

  • N – m x n stoichiometric matrix used such that P*N.

Author(s) Ronan Fleming