Mdfba

buildMDFBAProblem(model, varargin)[source]

Creates a MDFBA problem from the provided model.

USAGE:

LPproblem = buildMDFBAProblem (model, varargin)

INPUT:

model – A COBRA style model with the following fields:

  • .S - Stoichiometric Matrix

  • .lb - lower bounds

  • .ub - upper bounds

  • .b - metabolic constraints

  • .c - objective coefficients

  • .mets - metabolite identifiers

  • .csense - Constraint senses (optional, default Equality)

  • .osense - Optimisation sense (optional, default maximisation)

OPTIONAL INPUTS:

varargin – Variable arguments as parameter/value pairs:

  • ‘ignoredMets’ - Metabolites that do not need to be produced, even if used.

  • ‘minProd’ - the minimal production, if a metabolite is used, default(max(ub,abs(lb))/10000)

OUTPUT:

LPproblem – The MILPproblem structure representing the MDFBA problem

Note

Implementation based on description in: Benyamini et al. “Flux balance analysis accounting for metabolite dilution.” Genome Biol. 2010;11(4):R43. doi: 10.1186/gb-2010-11-4-r43

mdFBA(model, varargin)[source]

Solves an metabolic dilution FBA problem based on the given model

USAGE:

[sol, newActives] = mdFBA (model, varargin)

INPUT:

model – A COBRA style model with the following fields:

  • .S - Stoichiometric Matrix

  • .lb - lower bounds

  • .ub - upper bounds

  • .b - metabolic constraints

  • .c - objective coefficients

  • .mets - metabolite identifiers

  • .rxns - reaction identifiers

  • .csense - Constraint senses (optional, default Equality)

  • .osense - Optimisation sense (optional, default maximisation)

OPTIONAL INPUTS:

varargin – Variable arguments as parameter/value pairs

  • ‘ignoredMets’ - Metabolites that do not need to be produced, even if used.

  • ‘minProd’ - the minimal production, if a metabolite is used, default(max(ub,abs(lb))/10000)

  • ‘getInvalidSolution’ - whether to return an invalid solution, or retrieve an invalid solution that was obtained in an earlier run. If there is a solution from a previous run, no calculation will be performed! (default false)

OUTPUT:

sol – The solution of the MDFBA MILP with the following fields:

  • obj - objective value

  • solver - solver used

  • stat - the COBRA status

  • origStat - the original solver status

  • time - the time needed to solve the problem

  • full - the solution of the problem

  • additional field depending on the solver used, and whether an invalid solution is returned.

OPTIONAL OUTPUT:

newActives: Reactions that are only active in mdFBA

Note

Implementation based on description in: Benyamini et al. “Flux balance analysis accounting for metabolite dilution.” Genome Biol. 2010;11(4):R43. doi: 10.1186/gb-2010-11-4-r43