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.