Initialize ensemble

initializeEnsemble(ensemble, popIdx, verbose)

Initialize ensemble structure.

USAGE:

ensemble = initializeEnsemble(ensemble, popIdx, verbose)

INPUT:

ensemble (struct): model ensemble popIdx (int): population ID

OPTIONAL INPUT:

verbose (int): verbosity level

OUTPUT:

ensemble (struct): initialized model ensemble data structure

• description (char) : model name basically

• sampler (char) : specifies the sampling mode: GRASP or rejection

• solver (char) : which solver to use for the rejection sampler

• numConditions (int) : how many experimental conditions

• numStruct (int) : how many model structures

• numParticles (int) : how many models to be sampled

• parallel (int) : whether or not to parallelize sampling process

• numCores (int) : if parallel is true, how many cores to use

• alphaAlive (double) : percentage of alive models per iteration (SMC sampler only, not implemented yet)

• tolerance (double vector) : target tolerance vector

• S (int matrix) : stoichiometric matrix as defined in the input file

• rxns (char cell) : reaction IDs

• rxnNames (char cell) : reaction names

• exchRxns (int vector) : exchange reactions, marked as transport in rxns sheet

• activeRxns (int vector) : list with reactions marked as modeled

• isoenzymes (cell) : list with isoenzymes

• uniqueIso (cell) : list of unique isoenzymes

• mets (char cell) : metabolite IDs

• metNames (char cell) : metabolite names

• rxnMets (char cell) : names of reaction metabolites

• metsBalanced (int vector) : indices of balanced metabolites

• metsSimulated (int vector) : indices of simulated metabolites

• metsFixed (int vector) : which metabolites concentrations are defined as fixed (constant)

• Sred (int matrix) : reduced stoichiometric matrix, includes only balanced metabolites and active reactions

• measRates (double matrix) : measured reaction fluxes means

• measRatesStd (double matrix) : measured reaction fluxes standard deviations

• poolConst (vector) : coefficients with pool constraints

• ineqThermoConst (vector) : coefficients of thermodynamic inequeality constraints

• expFluxes (double vector) : experimental fluxes mean

• expFluxesStd (double vector) : experimental fluxes standard deviations

• fluxRef (double vector) : reference reaction fluxes means

• fluxRefStd (double vector) : reference reaction fluxes standard deviations

• freeFluxes (int vector) : free flux variables

• simWeights (double vector) : flux weights for the computation of the data and model discrepancies

• Sthermo (int matrix) : stoichiometric matrix used for thermodynamics, excludes exchange reactions

• gibbsRanges (double matrix) : thermodynamically feasible ranges for Gibbs energies

• metRanges (double matrix) : thermodynamically feasible ranges for metabolite concentrations

• G0Ranges (double matrix) : thermodynamically feasible ranges for standard Gibbs energies

• metsDataMin (double vector) : minimum value for scaled metabolite concentrations

• metsDataMax (double vector) : maximum value for scaled metabolite concentrations

• metsDataMean (double vector) : mean value for scaled metabolite concentrations

• prevPrior (cell) : previous prior for kinetic parameters (not implemented)

• prevPriorInfo (cell) : information about previous prior (not implemented)

• allosteric (cell) : which reactions are allosterically regulated

• subunits (int cell) : number of enzyme subunits for each reaction

• rxnMechanisms (char cell) : reaction mechanisms

• extremePathways (int cell) : extreme pathways for the given reaction mechanism

• inhibitors (char cell) : reaction inhibitors

• activators (char cell) : reaction activators

• negEffectors (char cell) : allosteric inhibitors

• posEffectors (char cell) : allosteric activators

• subOrder (char cell) : substrate binding order

• prodOrder (char cell) : product release order

• promiscuity (int cell) : promiscuous reactions

• kinActRxns (int vector) : kinetically active reactions, includes all reactions with mechanism other than fixedExchange

• prodDataMin (double vector) : minimum value for scaled enzyme concentrations

• prodDataMax (double vector) : maximum value for scaled enzyme concentrations

• prodDataMean (double vector) : mean value for scaled enzyme concentrations

• kinInactRxns (int vector) : kinetically inactive reactions, basically reactions with a fixedExchange mechanism

• fixedExch (double matrix) : fixed exchange reactions

• kineticFxn (char cell) : name of kinetic function used to build the model with all rate laws

• metLists (char cell) : list of metabolites (as defined in patterns) for each reaction

• revMatrix (int matrix) : reversibility matrix for elementary reaction mechanisms

• forwardFlux (int cell) : link matrix of elementary reaction steps

• Nelem (int cell) : null space basis matrix of the stoichiometric matrix of the reaction mechanism

• freeVars (char cell) : free variables

• metsActive (int vector) : active metabolite indices

• eigThreshold (double) : threshold for the real part of the jacobian eigenvalues, if there is any higher than the threshold the model is discarded

• thermoActive (int vector) : thermodynamically active reactions

• populations (struct) : structure with intermediate model populations (only required for SMC sampler, not implemented yet)

  • probParams (struct)

    • rxnParams (struct) : reaction parameters

      • alphaEnzymeAbundances (int vector) : hyperparameters for enzyme abundances (currently not used)

      • alphaReversibilities (int vector) : hyperparameters for microscopic reversibilities (currently not used)

      • betaModifierElemeFlux (int vector) : hyperparameters for elementary flux sampling (currently not used)

      • betaBranchFactor (int vector) : hyperparameters for branching factors (currently not used)

  • weights (double vector) : model weights (only for SMC, not implemented yet)

  • models (struct) : models in the ensemble

    • poolFactor (double vector) : hyperparameters for pool constraints

    • rxnParams (struct) : reaction parameters

      • reversibilities (double vector) : sampled elementary reaction reversibilities

      • enzymeAbundances (double vector) : sampled enzyme intermediates abundances

      • branchFactor (double vector) : sampled branching factor (for branched mechanisms only)

      • modifierElemeFlux (double vector) : sampled elementary flux for mechanisms with modifiers (inhibitors, activators)

      • allostericFactors (double vector) : sampled enzyme intermediates bound to allosteric effectors

      • L (double vector) : sampled allosteric constant

      • KnegEff (double vector) : sampled allosteric effector (negative) constant

      • KposEff (double vector) : sampled allosteric effector (positive) constant

• replenished particles (int) : number of models that are to be replenished in each iteration (only for SMC sampler, not implemented yet)