Ufba

buildUFBAmodel(model, variables)[source]

Integrates intracellular/extracellular metabolite measurements with COBRA model for flux balance analysis

  1. removing all exchange reactions (retains sinks and demands)

  2. setting rate of change of measured metabolites

  3. 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 INPUTS

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

OUTPUTS

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