FASTCORE

LP3(J, model, LPproblem, basis)

CPLEX implementation of LP-3 for input set J (see FASTCORE paper)

Usage

[V, basis] = LP3(J, model, basis)

LP7(J, model, LPproblem, epsilon, basis)

CPLEX implementation of LP-7 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)

CPLEX implementation of LP-9 for input sets K, P (see FASTCORE paper)

Usage

V = LP9(K, P, model, epsilon)

LP9cvx(K, P, model, epsilon)

CPLEX implementation of LP-9 for input sets K, P (see FASTCORE paper)

Usage

V = LP9cvx(K, P, model, epsilon)

fastCoreWeighted(C, model, weights, epsilon)

Based on: The FASTCORE algorithm for context-specific 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: 1e-4; 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)

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

fastcore(model, core, epsilon, printLevel)

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 1e-4)
• 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 context-specific metbolic network models. PLoS Comput. Biol. 10, e1003424.’

findSparseMode(J, P, singleton, model, LPproblem, epsilon, basis)

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: 1e-4; 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)

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 context-specific 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: 1e-4; see Vlassis et al for more details)

Output

• Supp – Support or [] if no reaction from J can get flux above epsilon