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 - m x n stoichiometric matrix

• .lb - n x 1 lower bounds

• .ub - n x 1 upper bounds

• .rxns - n x 1 cell array of reaction identifiers

• .biomassRxnAbbr - biomass reaction 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)

INPUTS:

model – COBRA Toolbox model with fields:

• .S - m x n stoichiometric matrix

• .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)

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

USAGE:

[P, vertexBool, N] = extremePools (model, param)

INPUTS:

• model – COBRA model structure with fields:

  • .S - m x (n + k) stoichiometric matrix

  • .SConsistentRxnBool - (optional) (n + k) x 1 boolean indicating the n stoichiometrically consistent reactions

  • .SIntRxnBool - (optional) boolean of reactions heuristically thought to be mass balanced

  • .SIntMetBool - (optional) boolean of metabolites heuristically thought to be involved in mass balanced reactions

  • .description - (optional) string used to name the lrs files

• param – (optional) parameter structure with fields:

  • .positivity - {0, (1)} if param.positivity == 1, then positive orthant base

  • .inequality - {(0), 1} if param.inequality == 1, then use two inequalities rather than a single equality

  • .debug - {(0), 1} if param.debug == 0, delete the generated lrs files

  • .facetEnumeration - {(0), 1} 0 for vertex enumeration

OUTPUTS:

• 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 = 0