Qfca

QFCA(model, reduction, varargin)

QFCA computes the table of flux coupling relations and the list of blocked reactions for a metabolic network specified by its stoichiometric matrix and irreversible reactions and also returns the reduced metabolic network.

USAGE

[reduced_net, fctable, blocked] = QFCA (model, reduction [, 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

• reduction – logical indicating whether DCE-induced reductions should be carried out or not

OPTIONAL INPUT

solver – the LP solver to be used; the currently available options are either ‘gurobi’ or ‘linprog’ with the default value of ‘linprog’

OUTPUTS

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

• fctable – the resulting flux coupling matrix; for the choice of entries, we use the F2C2 convention for the sake of compatibility. The meaning of the entry (i, j) is:

  • 0 - uncoupled reactions

  • 1 - fully coupled reactions

  • 2 - partially coupled reactions

  • 3 - reaction i is directionally coupled to reaction j

  • 4 - reaction j is directionally coupled to reaction i

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

Example

% The following code uses QFCA to compute the table of flux coupling relations % and the list of blocked reactions for the E. coli core model and also returns % the reduced metabolic network. load(‘ecoli_core_model.mat’); [reduced_net, fctable, blocked] = QFCA(model, true, ‘linprog’);

Note

The directionallyCoupled function can be utilized as a stand-alone function to find fictitious metabolite certificates.

blockedReac(S, rev, rxns, solver)

blockedReac finds the blocked reactions and removes them from the network

USAGE

[S_reduced, rev_reduced, rxns_reduced, blocked] = blockedReac (S, rev, rxns, solver)

INPUTS

• S – the associated sparse stoichiometric matrix

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

• rxns – the cell array of reaction abbreviations

• solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and otherwise the default COBRA LP solver

OUTPUTS

• S_reduced – the reduced sparse stoichiometric matrix

• rev_reduced – the reduced reversibility vector

• rxns_reduced – the reduced reaction abbreviations

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

directionallyCoupled(S, rev, i, solver)

directionallyCoupled finds all the directionally coupled reactions to i

USAGE

[certificate, result] = directionallyCoupled (S, rev, i, solver)

INPUTS

• S – the associated sparse stoichiometric matrix

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

• i – the index of reaction to which others are directionally coupled

• solver – the LP solver to be used; the currently available options are ‘gurobi’, ‘linprog’, and otherwise the default COBRA LP solver

OUTPUTS

• certificate – the fictitious metabolite for the positive certificate; S.’*certificate will be the corresponding directional coupling equation

• result – the result returned by the LP solver; all the -1 entries are directionally coupled to reaction i and the other entries except i are zero

mergeFullyCoupled(S, rev, rxns, i, j, c)

mergeFullyCoupled merges the fully coupled pair of reactions (i, j)

USAGE

[S_reduced, rev_reduced, rxns_reduced] = mergeFullyCoupled (S, rev, rxns, i, j, c)

INPUTS

• S – the associated sparse stoichiometric matrix

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

• rxns – the cell array of reaction abbreviations

• i – the reaction which the other one will merge with and is not removed

• j – the reaction which will be merged into the other reaction

• c – the full coupling coefficient

OUTPUTS

• S_reduced – the reduced sparse stoichiometric matrix

• rev_reduced – the reduced reversibility vector

• rxns_reduced – the reduced reaction abbreviations