FASTCORE¶

LP3
(J, model, LPproblem, basis)[source]¶ CPLEX implementation of LP3 for input set J (see FASTCORE paper)
Usage
[V, basis] = LP3(J, model, basis)

LP7
(J, model, LPproblem, epsilon, basis)[source]¶ CPLEX implementation of LP7 for input set J (see FASTCORE paper). Maximises the number of feasible fluxes in J whose value is at least epsilon
Usage
[V, basis] = LP7( J, model, epsilon, basis)Inputs
 J – indicies of irreversible reactions
 model – model
 LPproblem – LP problem
 epsilon – tolerance
Outputs
 V – optimal steady state flux vector
 basis – basis

LP9
(K, P, model, LPproblem, epsilon)[source]¶ CPLEX implementation of LP9 for input sets K, P (see FASTCORE paper)
Usage
V = LP9(K, P, model, epsilon)

LP9cvx
(K, P, model, epsilon)[source]¶ CPLEX implementation of LP9 for input sets K, P (see FASTCORE paper)
Usage
V = LP9cvx(K, P, model, epsilon)

fastCoreWeighted
(C, model, weights, epsilon)[source]¶ Based on: The FASTCORE algorithm for contextspecific metabolic network reconstruction, Vlassis et al., 2013, PLoS Comp Biol.
Usage
A = fastCoreWeighted( C, model, epsilon )Input
 C – List of reaction numbers corresponding to the core set
model Model structure, weights Weight vector for each reaction in the model
epsilon: Parameter (default: 1e4; see Vlassis et al for more details)Output
 A – A most compact model consistent with the applied constraints and containing the desired core set reactions (as given in C)

fastcc
(model, epsilon, printLevel, modeFlag, method)[source]¶ The FASTCC algorithm for testing the consistency of a stoichiometric model. Output A is the consistent part of the model [A,V] = fastcc(model, epsilon, printLevel)
Usage
[A, modelFlipped, V] = fastcc(model, epsilon, printLevel, modeFlag, method)Inputs
 model –
cobra model structure containing the fields:
 S  m x n stoichiometric matrix
 lb  n x 1 flux lower bound
 ub  n x 1 flux uppper bound
 rxns  n x 1 cell array of reaction abbreviations
 epsilon – smallest flux that is considered nonzero
 printLevel – 0 = silent, 1 = summary, 2 = debug
Optional inputs
 modeFlag – {(0),1}; 1=return matrix of modes V
 method – ‘original’  default or ‘nonconvex’
Outputs
 A – n x 1 boolean vector indicating the flux consistent reactions
 V – n x k matrix such that S(:,A) * V(:,A) = 0 and V(:,A)’ * 1 > 0
 model –
cobra model structure containing the fields:

fastcore
(model, core, epsilon, printLevel)[source]¶ Use the FASTCORE algorithm (‘Vlassis et al, 2014’) to extract a context specific model. FASTCORE algorithm defines one set of core reactions that is guaranteed to be active in the extracted model and find the minimum of reactions possible to support the core.
Usage
tissueModel = fastcore(model, core)Input
 model – (the following fields are required  others can be supplied) * S  m x 1 Stoichiometric matrix * lb  n x 1 Lower bounds * ub  n x 1 Upper bounds * rxns  n x 1 cell array of reaction abbreviations
 core: indices of reactions in cobra model that are part of the
 core set of reactions (called ‘C’ in ‘Vlassis et al, 2014’)
Optional inputs
 epsilon – smallest flux value that is considered nonzero (default 1e4)
 printLevel – 0 = silent, 1 = summary, 2 = debug (default  0)
Outputs
 tissueModel – extracted model
 coreRxnBool – n x 1 boolean vector indicating core reactions
‘Vlassis, Pacheco, Sauter (2014). Fast reconstruction of compact contextspecific metbolic network models. PLoS Comput. Biol. 10, e1003424.’

findSparseMode
(J, P, singleton, model, LPproblem, epsilon, basis)[source]¶ Finds a mode that contains as many reactions from J and as few from P. Returns its support, or [] if no reaction from J can get flux above epsilon
Usage
Supp = findSparseMode(J, P, singleton, model, LPproblem, epsilon)Inputs
 J – Indicies of irreversible reactions
 P – Reactions
 singleton – Takes only first instance from J, else takes whole J
 model – Model structure (for reference)
 LPproblem – LPproblem structure
 epsilon – Parameter (default: 1e4; see Vlassis et al for more details)
Optional input
 basis – Basis
Outputs
 Supp – Support or [] if no reaction from J can get flux above epsilon
 basis – Basis

findSparseModeWeighted
(J, P, singleton, model, LPproblem, weights, epsilon)[source]¶ Finds a mode that contains as many reactions from J and as few from P. Returns its support, or [] if no reaction from J can get flux above epsilon. Based on: The FASTCORE algorithm for contextspecific metabolic network reconstruction. Input C is the core set, and output A is the reconstruction, Vlassis et al., 2013, PLoS Comp Biol.
Usage
Supp = findSparseMode( J, P, singleton, model, epsilon )Inputs
 J – Indicies of irreversible reactions
 P – Reactions
 singleton – Takes only first instance from J, else takes whole J
 model – Model structure
 LPproblem – The LP problem for the model structure
 weights – The weights associated with the reactions.
 epsilon – Parameter (default: 1e4; see Vlassis et al for more details)
Output
 Supp – Support or [] if no reaction from J can get flux above epsilon