Load ensemble structure¶
- loadEnsembleStructure(xlsxFile)¶
Takes in an excel file and sets up the model ensemble data structure.
Also calculates reactions fluxes and Gibbs energies if wanted.
USAGE:
ensemble = loadEnsembleStructure(xlsxFile)
- INPUT:
xlsxFile (char): path to input excel file
- OUTPUT:
ensemble (struct): 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) : [TODO Pedro]
tolerance (double vector) : [TODO Pedro]
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 of the reaction mechanism
forwardFlux (int cell) : link matrix of enzyme intermediate (nodes) connections in the forward direction
Nelem (int cell) : null space basis of the stoichiometric matrix of elementary steps
freeVars (char cell) : free variables of the model
metsActive (int vector) : indices of metabolites participating in kinetic reactions
metsLi (int vector) : indices of linearly independent mass-balanced active metabolites