uFBA¶
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buildUFBAmodel
(model, variables)[source]¶ Integrates intracellular/extracellular metabolite measurements with COBRA model for flux balance analysis
- removing all exchange reactions (retains sinks and demands)
- setting rate of change of measured metabolites
- adding additional sinks to ensure the model simulates
Inputs
- model – COBRA model structure
- variables –
struct containing the following required fields:
- .metNames - cell array of mets for modification – those that have measurements (corresponding to model.mets)
- .changeSlopes - vector (length(metNames) x 1) that contains the rate of change (slope) of mets in metNames
- .changeIntervals - vector (length(metNames) x 1) that contains the 95% confidence interval of slopes in changeSlopes
- .ignoreSlopes - binary vector (length(metNames) x 1) that instructs specific slopes to be ignored (ignore if 1)
Optional input
- variables –
struct containing the following optional fields:
- .objRxn - objective reaction (corresponding to model.rxns)
- .metNoSink - cell array of metabolites that should not have a sink added, typically for mets where the concentration is known to be 0 (default = empty cell array, {})
- .metNoSinkUp - cell array of metabolites that should not have a sink added in the up direction (default = empty cell array, {})
- .metNoSinkDown - cell array of metabolites that should not have a sink added in the down direction (default = empty cell array, {})
- .conflictingMets - cell array of intracellular metabolites (corresponding to model.mets) that conflict with extracellular rates (default = empty cell array, {})
- .neededSinks - cell array of metabolites (corresponding to model.mets) that must have a sink at all times due to unknown degradation (default = empty cell array, {})
- .solvingStrategy - one of {‘case1’,’case2’,’case3’,’case4’,’case5’} (default = ‘case2’)
- .lambda - relaxation parameter (default = 1.5)
- .numIterations - number of iterations for the integer cut optimization method (default = 100)
- .timeLimit - time limit for solver (default = 30 seconds)
- .eWeight - weighting for preferential selection of extracellular sinks over intracellular (default= 1e6); if no weighting preferred, then set eWeight = 1
Output
- output –
struct containing the following outputs
- .model - constrained uFBA model
- .metsToUse - mets with measurements applied
- .relaxedNodes - cell array which contains which metabolites had a sink reaction added to model, the direction of the sink, and the bound of the sink reaction