mdFBA

buildMDFBAProblem(model, varargin)[source]

Creates a MDFBA problem from the provided model.

Usage

MDFBAProblem = 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
    • csense - Constraint senses (optional, default Equality)
    • osense - Optimisation sense (optional, default maximisation)

Optional input

  • 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

  • MDFBAProblem – 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] = 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
    • csense - Constraint senses (optional, default Equality)
    • osense - Optimisation sense (optional, default maximisation)

Optional input

  • 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