Metaboreport

generateMetaboReport(modelProperties, reportDir, orgNames)[source]

This function generates the metaboReport: an HTML report summarizing model properties and scores for one or more metabolic models, using reportTemplate.html as a template.

USAGE:

generateMetaboReport (modelProperties, reportDir, orgNames)

INPUTS:

  • modelProperties – Structure containing, for each model, the properties generated by generateMetaboScore (one field per model, each holding a modelProp2 substructure)

  • reportDir – Directory in which the generated modelreport_<ModelName>.html file(s) are saved

OPTIONAL INPUTS:

orgNames – Cell array of organism/model display names, one per field of modelProperties (default: falls back to the corresponding field name)

generateMetaboScore(model, nworkers)[source]

Analyzes metabolic model properties and generates scores. This function analyzes various aspects of the metabolic model, including basic properties, stoichiometric consistency, matrix conditioning, annotation of metabolites, reactions, genes, SBO terms, and generates overall scores for different aspects.

USAGE:

[modelProp, ScoresOverall] = generateMetaboScore (model, nworkers)

INPUTS:

model – Metabolic model structure (COBRA Toolbox format) with fields:

  • .S - m x n stoichiometric matrix

  • .rxns - n x 1 reaction identifiers

  • .mets - m x 1 metabolite identifiers

  • .genes - g x 1 gene identifiers

  • .grRules - n x 1 gene-protein-reaction rules

  • .lb - n x 1 lower flux bounds

  • .ub - n x 1 upper flux bounds

  • .metFormulas - m x 1 elemental formulas of metabolites

  • .metCharges - m x 1 metabolite charges

  • .SConsistentMetBool - m x 1 logical, true for stoichiometrically consistent metabolites (set by checkStoichiometricConsistency)

  • .SConsistentRxnBool - n x 1 logical, true for stoichiometrically consistent reactions (set by checkStoichiometricConsistency)

  • .SIntRxnBool - n x 1 logical, true for internal (non-exchange/demand/sink) reactions

  • .metSBOTerms - m x 1 SBO terms for metabolites (optional annotation field)

  • .rxnSBOTerms - n x 1 SBO terms for reactions (optional annotation field)

  • .geneSBOTerms - g x 1 SBO terms for genes (optional annotation field)

Additional optional annotation ID fields (e.g. .rxnKEGGID, .metChEBIID, .geneUniprotID) are read, when present, to compute annotation scores.

OPTIONAL INPUTS:

nworkers – Number of workers for parallel processing (default: 4)

OUTPUTS:

  • modelProp – Structure containing various properties of the metabolic model

  • ScoresOverall – Structure containing overall scores for different aspects

Example

[modelProp, ScoresOverall] = generateMetaboScore(model) [modelProp, ScoresOverall] = generateMetaboScore(model, 4)

populateModelwithRxnIDs(model)[source]

Populates a COBRA model with reaction cross-reference identifiers looked up from the VMH reaction list spreadsheet (shipped alongside this function) and, for rxnSEEDID, from a DEMETER seed-to-VMH translation table.

USAGE:

[modelUpdated] = populateModelwithRxnIDs (model)

INPUTS:

model – COBRA model structure

OUTPUT:

modelUpdated – COBRA model structure with the following reaction ID fields populated (overwritten where already present):

  • .rxnECNumbers - EC number(s) for the reaction

  • .rxnKEGGID - KEGG reaction identifier

  • .rxnMetaNetXID - MetaNetX reaction identifier

  • .rxnSEEDID - ModelSEED reaction identifier

  • .rxnRheaID - Rhea reaction identifier

tutorial_MetaboRePort[source]

MetaboRePort:

tutorial_MetaboRePort_APOLLO[source]

MetaboRePort:

tutorial_MetaboRePort_m[source]

MetaboRePort: