Reconstruction
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gapFind
(model, findNCgaps, verbFlag)[source]¶ Identifies all blocked metabolites (anything downstream of a gap) in a model. MILP algorithm that finds gaps that may be missed by simple inspection of the S matrix. To find every gap in a model, change the rxn bounds on all exchange reactions to allow uptake of every metabolite.
Usage
[allGaps, rootGaps, downstreamGaps] = gapFind(model, findNCgaps, verbFlag)Input
- model – a COBRA model
Optional inputs
- findNCgaps – find no consupmption gaps as well as no production gaps (default false)
- verbFlag – verbose flag (default false)
Outputs
- allGaps – all gaps found by GapFind
- rootGaps – all root no production (and consumption) gaps
- downstreamGaps – all downstream gaps
Based on Kumar, V. et al. BMC Bioinformatics. 2007 Jun 20;8:212.
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testPathway
(model, MetIn, MetOut, AdditionalMetsInorOut, ObjectiveOption)[source]¶ Allows the user to see if given one metabolite A, downstream metabolite B can be made made. Additional sinks can be added for co-factors if needed A –>–>–>–>–> B
Usage
[Flux, FBAsolution, model] = testPathway(model, MetIn, MetOut, AdditionalMetsInorOut, ObjectiveOption)Inputs
- model – COBRA model structure
- MetIn – The input metabolite(s) (A)
- MetOut – The output metabolite (B)
Optional inputs
- AdditionalMetsInorOut – Additional metabolites for which sinks will be added
- ObjectiveOption –
Boolean:
- 1 = objective will be production of B (default)
- 0 = use objective in model
Outputs
- Flux – The rate of B production
- FBAsolution – Solution to the FBA problem
- model – COBRA model with sinks in it