mdFBA¶
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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
- model –
A COBRA style model with the following fields:
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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
- model –
A COBRA style model with the following fields: