Transcriptomics

• SWIFTCORE
• FASTCORE
• MBA
• GIMME
• INIT
• iMAT
• Preprocessing

createTissueSpecificModel(model, options, funcModel, exRxnRemove, optionalParams)

Creates draft tissue specific model from mRNA expression data

USAGE:

tissueModel = createTissueSpecificModel(model, options)

INPUTS:

model: model strusture

options: structure field containing method specific

informations

.solver: Use either ‘GIMME’,’iMAT’,’INIT’,’MBA’,

‘mCADRE’,’fastCore’,’swiftcore’

. ‘additional parameters’: see section below entiteld OPTIONAL INPUTS SPECIFIC TO EACH MODEL EXTRACTION ALGORITHM

OPTIONAL INPUTS:

funcModel: 1 - Build a functional model having only reactions

that can carry a flux (using a consistency check), 0 - skip this step (Default = 0)

exRxnRemove: Names of exchange reactions to remove

(Default = [])

optionalParams Additional paramaters for the consistency

check. Will only be used if funcModel = 1 Is a structure with possible fields of epsilon (numeric, min nonzero mass), modeFlag (return flux mode, 0/1), and method (‘swiftcc’,’fastcc’,’dc’)

OUTPUTS:

tissueModel: extracted model

OPTIONAL INPUTS SPECIFIC TO EACH MODEL EXTRACTION ALGORITHM: This section describes the additional parameter fields that need to be set in ‘options’ structure depending on the solver used. Some of these are optional (marked by an ‘*’), if not defined, they will be set at their default values.

for iMAT

options.expressionRxns reaction expression, expression data corresponding to model.rxns.

Note : If no gene-expression data are available for the reactions, set the value to -1

options.threshold_lb lower bound of expression threshold, reactions with

expression below this value are “non-expressed”

options.threshold_ub upper bound of expression threshold, reactions with

expression above this value are “expressed”

options.tol* minimum flux threshold for “expressed” reactions

(default 1e-8)

options.core* cell with reaction names (strings) that are manually put in

the high confidence set (default - no core reactions)

options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’) options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling

flux (default 1)

for GIMME

options.expressionRxns reaction expression, expression data corresponding to model.rxns.

Note : If no gene-expression data are available for the reactions, set the value to -1

options.threshold expression threshold, reactions below this are minimized options.obj_frac* minimum fraction of the model objective function

(default - 0.9)

for INIT

options.weights column with positive (high expression) and negative

(low expression) weights for each reaction

options.tol* minimum flux threshold for “expressed” reactions

(default - 1e-8)

options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’)

options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling

flux (default 1)

for MBA

options.medium_set list of reaction names with medium confidence options.high_set list of reaction names with high confidence options.tol* minimum flux threshold for “expressed” reactions

(default - 1e-8)

for mCADRE

options.ubiquityScore ubiquity scores, vector of the size of ‘model.rxns’

quantifying how often a gene is expressed accross samples.

options.confidenceScores literature-based evidence for generic model,

vector of the size of ‘model.rxns’

options.protectedRxns* cell array with reactions names that are manually added to

the core reaction set (default- no reactions)

options.checkFunctionality* Boolean variable that determine if the model should be able

to produce the metabolites associated with the protectedRxns

0: don’t use functionality check (default value) 1: include functionality check

options.eta* tradeoff between removing core and zero-expression

reactions (default - 1/3)

options.tol* minimum flux threshold for “expressed” reactions

(default - 1e-8)

for fastCore

options.core indices of reactions in cobra model that are part of the

core set of reactions

options.epsilon* smallest flux value that is considered

nonzero (default getCobraSolverParams(‘LP’, ‘feasTol’)*100)

options.printLevel* 0 = silent, 1 = summary, 2 = debug (default 0)

for swiftcore

options.core indices of reactions in cobra model that are part of the

core set of reactions

options.tol* smallest flux value that is considered nonzero (default 1e-10) options.reduction* boolean enabling the metabolic network reduction preprocess options.weights* weight vector for the penalties associated with each reaction options.LPsolver* the LP solver to be used; the currently available options are

‘gurobi’, ‘linprog’, and ‘cplex’ with the default value of ‘gurobi’. It fallbacks to the COBRA LP solver interface if another supported solver is called or ‘gurobi’ is not available.

for thermoKernel