Swiftcore

blocked(S, rev, solver)[source]

blocked finds all the irreversible blocked reactions and is utilized in swiftcc

USAGE

result = blocked (S, rev, solver)

INPUTS

  • S – the associated sparse stoichiometric matrix

  • rev – the 0-1 vector with 1’s corresponding to the reversible reactions

  • solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘linprog’. It fallbacks to the COBRA LP solver interface if another supported solver is called.

OUTPUT

result – the result returned by the LP solver; among the last n entries, all the -1 entries are blocked, and the other entries are zero. The first m entries are its fictitious metabolite certificate.

core(model, blocked, weights, solver)[source]

core finds a feasible flux distribution to unblock a given list of blocked reactions and is utilized in swiftcore

USAGE

flux = core (S, rev, blocked, weights, solver)

INPUTS

  • model – the metabolic network with fields: * .S - the associated sparse stoichiometric matrix * .rev - the 0-1 indicator vector of the reversible reactions * .rxns - the cell array of reaction abbreviations * .mets - the cell array of metabolite abbreviations

  • blocked – the 0-1 vector with 1’s corresponding to the blocked reactions

  • weights – weight vector for the penalties associated with each reaction

  • solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘linprog’. It fallbacks to the COBRA LP solver interface if

    another supported solver is called.

OUTPUT

flux – a feasible flux distribution

partition(model, solver, algorithm)[source]

swiftcc++ and fastcc++ augment swiftcc and fastcc by this preprocess

USAGE

component = partition (model, solver, algorithm)

INPUTS

  • model – the metabolic network reconstruction * .S - the associated sparse stoichiometric matrix * .lb - feasible flux distribution lower bound * .ub - feasible flux distribution uppper bound * .rxns - cell array of reaction abbreviations * .rev - the 0-1 indicator vector of the reversible reactions

  • solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘linprog’. It fallbacks to the COBRA LP solver interface if another supported solver is called.

  • algorithm – the backend algorithm to be utilized between ‘swift’ and ‘fast’

OUTPUT

component – the index set of the reactions constituting the maximum flux consistent metabolic subnetwork

Note

requires bioinformatics toolbox

swiftcc(S, rev, varargin)[source]

swiftcc is an even faster version of fastcc

USAGE

consistent = swiftcc (S, rev [, solver])

INPUTS

  • S – the associated sparse stoichiometric matrix

  • rev – the 0-1 vector with 1’s corresponding to the reversible reactions

OPTIONAL INPUT

solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘linprog’. It fallbacks to the COBRA LP solver interface if another supported solver is called.

OUTPUT

consistent – the 0-1 indicator vector of the reactions constituting the maximum flux consistent metabolic subnetwork

swiftcore(model, coreInd, weights, tol, reduction, varargin)[source]

swifcore is an even faster version of fastcore

USAGE

[reconstruction, reconInd, LP] = swiftcore (model, coreInd, weights, tol, reduction, solver)

INPUTS

  • model – the metabolic network with fields: * .S - the associated sparse stoichiometric matrix * .lb - lower bounds on reaction rates * .ub - upper bounds on reaction rates * .rxns - the cell array of reaction abbreviations * .mets - the cell array of metabolite abbreviations

  • coreInd – the set of indices corresponding to the core reactions

  • weights – the weight vector for the penalties associated with each reaction

  • tol – zero-tolerance, i.e., the smallest flux value considered nonzero

  • reduction – boolean enabling the metabolic network reduction preprocess

OPTIONAL INPUT

solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘linprog’. It fallbacks to the COBRA LP solver interface if another supported solver is called.

OUTPUTS

  • reconstruction – the flux consistent metabolic network reconstructed from the core reactions

  • reconInd – the 0-1 indicator vector of the reactions constituting the reconstruction

  • LP – the number of solved LPs

Note

For the choice of the weight vector, use c*ones(n, 1) where c is an arbitrary constant c > 1 if you have no preference over reactions. Also, note that the input model is assumed to be flux consistent.