- gapFind(model, findNCgaps, verbFlag)¶
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.
- testPathway(model, MetIn, MetOut, AdditionalMetsInorOut, ObjectiveOption)¶
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