Refinement

addRefinementComments(model, summary)[source]

Adds descriptions to the model.comments field based on refinement performed by the DEMETER pipeline

USAGE:

model = addRefinementComments (model, summary)

INPUTS:

  • model – COBRA model structure with fields:

    • .grRules - Gene-protein-reaction rules; read to detect and clear temporary gap-filling/refinement labels

    • .rxns - Reaction identifiers; read to detect exchange (EX_), demand (DM_), and sink (sink_) reactions

  • summary – Structure with information on refinement performed on the model, with fields:

    • .conditionSpecificGapfill - Reactions added during condition-specific gapfilling

    • .targetedGapfill - Reactions added during targeted gapfilling

    • .relaxFBAGapfill - Reactions added by relaxFBA

    • .addedReactionsBiomass - Reactions added to enable synthesis of biomass components according to the gram status of the organism

OUTPUT:

model – COBRA model structure with fields:

  • .comments - Reaction comments describing how each reaction was added or refined during DEMETER refinement

  • .rxnConfidenceScores - Reaction confidence scores set according to refinement provenance

  • .grRules - Temporary gap-filling/refinement labels removed

anaerobicGrowthGapfill(model, biomassReaction, database)[source]

Tests if the input microbe model can grow anaerobically and gap-fills by adding anaerobic co-factor utilizing reactions.

USAGE:

[model, oxGapfillRxns, anaerGrowthOK] = anaerobicGrowthGapfill (model, biomassReaction, database)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - reaction identifiers

    • .mets - metabolite identifiers

    • .lb - lower flux bounds

  • biomassReaction – Biomass reaction abbreviation

  • database – rBioNet reaction database with fields:

    • .reactions - cell array with min. 3 columns: column 1 reaction abbreviation, column 2 reaction name, column 3 reaction formula

OUTPUTS:

  • model – COBRA model structure, gap-filled with the reactions needed for anaerobic growth if applicable

  • oxGapfillRxns – List of reactions added to enable anaerobic growth

  • anaerGrowthOK – Boolean indicating whether the model could be gap-filled to grow anaerobically (1) or not (0)

carbonSourceGapfill(model, microbeID, database, inputDataFolder)[source]

Gap-fills carbon source utilization pathways in a microbial reconstruction based on experimental evidence.

USAGE:

[model, addedRxns, removedRxns] = carbonSourceGapfill (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - reaction identifiers, used to check for reactions already present

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - cell array with min. 3 columns: column 1 reaction abbreviation, column 2 reaction name, column 3 reaction formula

  • inputDataFolder – Folder with experimental data and database files to load

OUTPUTS:

  • model – COBRA model structure refined through experimental data for carbon sources

  • addedRxns – List of reactions that were added during refinement

  • removedRxns – List of reactions that were removed during refinement

connectRxnGapfilling(model, database)[source]

Part of the DEMETER pipeline. This function adds reactions to unblock specific pathways.

USAGE:

[resolveBlocked, model] = connectRxnGapfilling (model, database)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .mets - Metabolite identifiers

    • .c - Objective coefficients

  • database – rBioNet reaction database structure with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), reaction name (column 2), and reaction formula (column 3)

OUTPUTS:

  • resolveBlocked – List of reactions added to unblock previously blocked pathways

  • model – COBRA model structure with unblocking reactions added

createPeriplasmaticSpace(model, microbeID, infoFile)[source]

Part of the DEMETER pipeline. This function creates a periplasmatic space for refined reconstructions if it is appropriate for the organism. The periplasmatic space is created by by retrieving all extracellular metabolites and adding a third compartment.

USAGE:

[model] = createPeriplasmaticSpace (model, microbeID, infoFile)

INPUTS:

  • model – COBRA model structure with fields:

    • .mets - Metabolite identifiers

    • .metNames - Metabolite names

    • .metFormulas - Elemental formulas

    • .metCharges - Metabolite charges

    • .rxns - Reaction identifiers

    • .rxnNames - Reaction names

    • .lb - Lower bounds

    • .ub - Upper bounds

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • infoFile – Table with taxonomic and gram staining information on microbes to reconstruct

OUTPUTS:

model – COBRA model structure with a periplasmatic compartment added, if appropriate for the organism

createSBMLFiles(refinedFolder, sbmlFolder)[source]

Creates SBML files for the created refined reconstructions. This may be time-consuming.

USAGE:

createSBMLFiles (refinedFolder, sbmlFolder)

INPUTS:

  • refinedFolder – Folder with refined COBRA models generated by the refinement pipeline

  • sbmlFolder – Folder where SBML files, if desired, will be saved

curateAgainstBacDiveData(model, microbeID, database, inputDataFolder)[source]

Gap-fills and/or removes reactions in a genome-scale reconstructions based on data from BacDive (https://bacdive.dsmz.de).

USAGE:

[model, addedRxns, removedRxns] = curateAgainstBacDiveData (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .grRules - Readable gene-protein-reaction rules

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database structure with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), reaction name (column 2), and reaction formula (column 3)

  • inputDataFolder – Folder with experimental data and database files to load

OUTPUTS:

  • model – COBRA model structure refined through BacDive data

  • addedRxns – List of reactions that were added during refinement

  • removedRxns – List of reactions that were removed during refinement

curateGrowthRequirements(model, microbeID, database, inputDataFolder)[source]

Takes the growth requirements of an organism (if known) as input and refines the reconstruction accordingly. Reactions are gap-filled and/or delete to reconcile mismatches between experimental and in silico metabolite essentiality. These curation steps were determined manually. The first step is printing the organism’s biomass components and subsequent evaluation which ones are required/ not required by the model. There are four possible cases: 1) essential in vivo and not in BOF -> add to BOF and add transporter/ remove unannotated biosynthesis reactions 2) essential in vivo and in BOF -> add transporter/ remove unannotated biosynthesis reactions 3) nonessential in vivo and not in BOF -> OK 4) nonessential in vivo and in BOF -> if pathway is mostly present: gapfill. If pathway is not present: remove from BOF

USAGE:

[model, addedMismatchRxns, deletedMismatchRxns] = curateGrowthRequirements (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .grRules - Gene-protein-reaction rules, used to identify reactions that have already been gap-filled or are unannotated

    • .lb - Reaction lower bounds

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), name (column 2), and formula (column 3)

  • inputDataFolder – Folder with input tables with experimental data and databases that inform the refinement process

OUTPUTS:

  • model – COBRA model structure with fields:

    • .comments - Reaction comments describing how each added reaction was gap-filled

    • .citations - Reaction literature citations, set empty for newly added reactions

    • .rxnECNumbers - Reaction EC numbers, set empty for newly added reactions

    • .rxnKEGGID - Reaction KEGG identifiers, set empty for newly added reactions

    • .rxnConfidenceScores - Reaction confidence scores, set to 0 for newly added reactions

    • .grRules - Gene-protein-reaction rules, set to GrowthRequirementsGapfill for newly added reactions

  • addedMismatchRxns – Reactions added to conform to growth requirements

  • deletedMismatchRxns – Reactions deleted to conform to growth requirements

deleteSeedGapfilledReactions(model, biomassReaction)[source]

Part of the DEMETER pipeline. Deletes reactions gapfilled by the Model SEED pipeline that are no longer needed after the reconstruction was refined.

USAGE:

[model, deletedSEEDRxns] = deleteSeedGapfilledReactions (model, biomassReaction)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - reaction identifiers

    • .grRules - gene-protein-reaction rules, used to identify reactions gap-filled by the SEED pipeline

  • biomassReaction – Biomass reaction abbreviation

OUTPUTS:

  • model – COBRA model structure with the no-longer-needed SEED gap-filled reactions removed

  • deletedSEEDRxns – List of deleted gapfilled reactions

doubleCheckGapfilledReactions(model, summary, biomassReaction, microbeID, database, definedMediumGrowthOK, inputDataFolder)[source]

Part of the DEMETER pipeline. Deletes reactions gapfilled by DEMETER that are no longer needed after finishing all steps of the pipeline.

USAGE:

[model, summary] = doubleCheckGapfilledReactions (model, summary, biomassReaction, microbeID, database, definedMediumGrowthOK, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .grRules - Gene-protein-reaction rules, used to identify reactions gap-filled by DEMETER (grRule demeterGapfill)

    • .rxns - Reaction identifiers

  • summary – Structure with information on refinement performed on the model, with fields:

    • .conditionSpecificGapfill - Reactions added during condition-specific gapfilling

    • .targetedGapfill - Reactions added during targeted gapfilling

    • .relaxFBAGapfill - Reactions added by relaxFBA

    • .futileCycles_addedRxns - Reactions added to remove futile cycles

    • .addedMismatchRxns - Reactions added to conform to growth requirements

    • .addedReactionsBiomass - Reactions added to enable synthesis of biomass components according to the gram status of the organism

  • biomassReaction – Biomass reaction abbreviation

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database containing min. 3 columns: Column 1: reaction abbreviation, Column 2: reaction name, Column 3: reaction formula.

  • definedMediumGrowthOK – If 1, defined medium is available for the organism and the model can grow on it

  • inputDataFolder – Folder with experimental data and database files to load

OUTPUTS:

  • model – COBRA model structure with unneeded gapfilled reactions removed

  • summary – Structure with information on refinement performed on the model, updated with the reactions removed during double-checking

fermentationPathwayGapfill(model, microbeID, database, inputDataFolder)[source]

Gap-fills fermentation pathways in a microbial reconstruction based on experimental evidence.

USAGE:

[model, addedRxns, removedRxns] = fermentationPathwayGapfill (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .grRules - Gene-protein-reaction rules, used to identify reactions that have already been gap-filled or are unannotated

    • .rxns - Reaction identifiers, used to determine which pathway reactions are already present

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), name (column 2), and formula (column 3)

  • inputDataFolder – Folder with input tables with experimental data on fermentation pathways that inform the refinement process

OUTPUTS:

  • model – COBRA model structure with gap-filled fermentation pathway reactions

  • addedRxns – List of reactions that were added during refinement

  • removedRxns – List of reactions that were removed during refinement

findTransportersWithoutExchanges(model)[source]

Part of the DEMETER pipeline. Finds transporters to extracellular space that are blocked because they have no exchange reaction associated with them.

USAGE:

[model, transportersWithoutExchanges] = findTransportersWithoutExchanges (model)

INPUTS:

model – COBRA model structure with fields:

  • .mets - Metabolite identifiers

  • .rxns - Reaction identifiers

  • .subSystems - Subsystem annotations

OUTPUTS:

  • model – COBRA model structure with blocked transporters removed

  • transportersWithoutExchanges – Removed transport reactions

findUnusedExchangeReactions(model)[source]

Part of the DEMETER pipeline. Finds exchange reactions that are no longer used and should be deleted after deleting unnecessary transport reactions gapfilled by Model SEED.

USAGE:

[model, unusedExchanges] = findUnusedExchangeReactions (model)

INPUTS:

model – COBRA model structure with fields:

  • .rxns - Reaction identifiers

OUTPUTS:

  • model – COBRA model structure with unused exchange reactions removed

  • unusedExchanges – Removed unused exchange reactions

performDataDrivenRefinement(model, microbeID, biomassReaction, database, inputDataFolder, summary)[source]

This function is part of the DEMETER pipeline and performs data-driven refinement of a genome-scale reconstruction based on available species-specific experimental data.

USAGE:

[refinedModel, summary] = performDataDrivenRefinement (model, microbeID, biomassReaction, database, inputDataFolder, summary)

INPUTS:

  • model – COBRA model structure to refine, with fields:

    • .rxns - Reaction identifiers

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • biomassReaction – Biomass reaction abbreviation

  • database – Structure containing the reaction and metabolite database, with fields:

    • .metabolites - cell array of metabolite data (abbreviation, name, …)

  • inputDataFolder – Folder with input tables with experimental data and databases that inform the refinement process

  • summary – Structure with information on refinement performed so far, extended in place with one field per refinement step run by this function

OUTPUTS:

  • refinedModel – Refined COBRA model structure

  • summary – Structure with information on performed refinement

putrefactionPathwaysGapfilling(model, microbeID, database)[source]

This function adds exchange, transport and biosynthesis reactions for putrefaction pathways according to data collected from Ref. PMID:29163445 as part of the DEMETER pipeline.

USAGE:

[model, rxnsAdded] = putrefactionPathwaysGapfilling (model, microbeID, database)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - reaction identifiers

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - cell array with min. 3 columns: column 1 reaction abbreviation, column 2 reaction name, column 3 reaction formula

OUTPUTS:

  • model – COBRA model structure with added putrefaction pathway reactions, if applicable

  • rxnsAdded – Reactions added based on experimental data

rebuildBiomassReaction(model, microbeID, biomassReaction, database, infoFile)[source]

Part of the DEMETER pipeline. This function rebuilds the biomass objective function of the reconstruction based on taxonomical information for the organism. The biomass formulation is based on gram-staining, taxonomy (Bacteria vs. Archaea), and phylum-specific features.

USAGE:

[model, removedBioComp, addedReactionsBiomass] = rebuildBiomassReaction (model, microbeID, biomassReaction, database, infoFile)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .mets - Metabolite identifiers

    • .S - Stoichiometric matrix

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • biomassReaction – Biomass reaction abbreviation

  • database – Structure containing the reaction and metabolite database, with fields:

    • .reactions - cell array of reaction data (abbreviation, name, reaction formula, …)

  • infoFile – Cell array (with header row) of taxonomic and gram-staining information on microbes to reconstruct

OUTPUTS:

  • model – COBRA model structure with the biomass objective function rebuilt

  • removedBioComp – Removed components that should not be in the biomass objective function (BOF)

  • addedReactionsBiomass – Reactions that were added to enable flux through the rebuilt BOF

rebuildModel(model, database, biomassReaction)[source]

Rebuilds a genome-scale reconstruction with Virtual Metabolic Human (VMH) metabolic and reaction nomenclature while ensuring quality control through rBioNet.

USAGE:

[rebuiltModel] = rebuildModel (model, database, biomassReaction)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .rxnNames - Reaction names

    • .grRules - Readable gene protein reaction rules

    • .subSystems - Subsystem annotations

    • .lb - Lower bounds

    • .ub - Upper bounds

    • .formulas - Reaction formula strings

    • .citations - Literature citation(s) associated with each reaction

    • .comments - Free-text comment associated with each reaction

    • .rxnECNumbers - EC numbers

    • .rxnKEGGID - KEGG reaction identifiers

    • .rxnConfidenceScores - Reaction confidence scores

    • .metPubChemID - PubChem identifiers

    • .metChEBIID - ChEBI identifiers

    • .metKEGGID - KEGG metabolite identifiers

    • .description - provenance sub-structure populated with .author and .date by this function

  • database – Structure containing rBioNet reaction and metabolite database, with fields:

    • .reactions - cell array of reaction data (abbreviation, name, reaction formula, reversibility flag, …, subsystem)

OPTIONAL INPUTS:

biomassReaction – Biomass reaction abbreviation (if needs to be specified, otherwise, will be inferred automatically)

OUTPUTS:

rebuiltModel – Quality-controlled COBRA model structure

refineGenomeAnnotation(model, microbeID, database, inputDataFolder)[source]

Part of the DEMETER pipeline. Refines a reconstruction based on comparative genomics data retrieved from PubSEED spreadsheets. Adds reactions linked to genes that were found in the respective organisms based on manual comparative genomic analyses. If the reaction is already present, the gene-protein-reaction association (GPR) is updated.

USAGE:

[model, addAnnRxns, updateGPRCnt] = refineGenomeAnnotation (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - reaction identifiers

    • .grRules - gene-protein-reaction rules

    • .comments - free-text comment for the reaction

    • .citations - literature citation for the reaction

    • .rxnECNumbers - EC numbers

    • .rxnKEGGID - KEGG reaction identifiers

    • .rxnConfidenceScores - reaction confidence scores

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - cell array with min. 3 columns: column 1 reaction abbreviation, column 2 reaction name, column 3 reaction formula

  • inputDataFolder – Folder with experimental data and database files to load

OUTPUTS:

  • model – COBRA model structure, refined based on comparative genomics data if applicable

  • addAnnRxns – Reactions newly added based on comparative genomics data

  • updateGPRCnt – Reactions for which GPRs were updated based on comparative genomics data

refinementPipeline(model, microbeID, infoFilePath, inputDataFolder, translateModels)[source]

This function runs the semi-automatic refinement pipeline on a draft reconstruction generated by the KBase pipeline or a previously refined reconstruction.

USAGE:

[refinedModel, summary] = refinementPipeline (model, microbeID, infoFilePath, inputDataFolder, translateModels)

INPUTS:

  • model – COBRA model structure to refine, with fields:

    • .rxns - Reaction identifiers

    • .mets - Metabolite identifiers

    • .lb - Lower bounds

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • infoFilePath – File with information on reconstructions to refine

  • inputDataFolder – Folder with input tables with experimental data and databases that inform the refinement process

OPTIONAL INPUTS:

translateModels – Boolean indicating whether to translate models if they are in KBase nomenclature (default: true)

OUTPUTS:

  • refinedModel – COBRA model structure refined through the AGORA refinement pipeline

  • summary – Structure aggregating the results of each performed refinement step (e.g., reactions added or removed by gap-filling, biomass rebuild, and annotation curation), with one field per refinement step

removeUnannotatedReactions(model, microbeID, biomassReaction, growsOnDefinedMedium, inputDataFolder)[source]

Part of the DEMETER pipeline. Refines a reconstruction based on comparative genomics data retrieved from PubSEED spreadsheets. Removes reactions that were present in the reconstruction before refinement but that are not annotated in the organism according to manually performed comparative genomic analyses.

USAGE:

[model, rmUnannRxns] = removeUnannotatedReactions (model, microbeID, biomassReaction, growsOnDefinedMedium, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • biomassReaction – Biomass reaction abbreviation

  • growsOnDefinedMedium – If 1, defined medium is available for the organism and the model can grow on it

  • inputDataFolder – Folder with experimental data and database files to load

OUTPUTS:

  • model – COBRA model structure with unannotated reactions removed

  • rmUnannRxns – Removed reactions based on comparative genomics data

runDemeter(draftFolder, varargin)[source]

This function runs the DEMETER pipeline consisting of three steps: 1) refining all draft reconstructions, 2) testing the refined reconstructions against the input data, 3) preparing a report detailing any additional debugging that needs to be performed.

USAGE:

[reconVersion, refinedFolder, translatedDraftsFolder, summaryFolder] = runDemeter (draftFolder, varargin)

INPUTS:

draftFolder – Folder with draft COBRA models generated by KBase pipeline to analyze

OPTIONAL INPUTS:

  • translateModels – Boolean indicating whether to translate models if they are in KBase nomenclature (default: true)

  • refinedFolder – Folder with refined COBRA models generated by the refinement pipeline

  • translatedDraftsFolder – Folder with draft COBRA models with translated nomenclature and stored as mat files

  • infoFilePath – File with information on reconstructions to refine

  • inputDataFolder – Folder with experimental data and database files to load

  • summaryFolder – Folder with information on performed gapfilling and refinement

  • reconVersion – Name of the refined reconstruction resource (default: “Reconstructions”)

  • numWorkers – Number of workers in parallel pool (default: 2)

  • createSBML – Defines whether refined reconstructions should be exported in SBML format (default: false)

OUTPUTS:

  • reconVersion – Name of the refined reconstruction resource (default: “Reconstructions”)

  • refinedFolder – Folder with refined COBRA models generated by the refinement pipeline

  • translatedDraftsFolder – Folder with draft COBRA models with translated nomenclature and stored as mat files

  • summaryFolder – Folder with information on performed gapfilling and refinement

secretionProductGapfill(model, microbeID, database, inputDataFolder)[source]

This function adds exchange, transport and biosynthesis reactions for experimentally shown secreted metabolites according to data collected for the DEMETER pipeline.

USAGE:

[model, secretionRxnsAdded] = secretionProductGapfill (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database structure with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), reaction name (column 2), and reaction formula (column 3)

  • inputDataFolder – Folder with input tables with experimental data and databases that inform the refinement process

OUTPUTS:

  • model – COBRA model structure with added pathways if applies

  • secretionRxnsAdded – Reactions added based on experimental data

translateDraftReconstruction(model)[source]

This function translates reaction and metabolite IDs in KBase draft reconstructions to VMH nomenclature so the test suite can be performed on them. It does not make changes to the reaction content otherwise.

USAGE:

[translatedModel] = translateDraftReconstruction (model)

INPUTS:

model – COBRA model structure generated by the KBase reconstruction pipeline, with fields:

  • .mets - metabolite identifiers

  • .rxns - reaction identifiers

  • .rxnNames - reaction names

  • .lb - lower flux bounds

  • .ub - upper flux bounds

  • .grRules - gene-protein-reaction rules

  • .metFormulas - elemental formulas of metabolites

  • .metCharges - metabolite charges

OUTPUTS:

translatedModel – COBRA model structure with metabolites and reactions translated to VMH identifiers (but not ran through refinement pipeline)

translateKBaseModel2VMHModel(model, biomassReaction, database)[source]

Translates reaction and metabolite identifiers from a KBase/ModelSEED reconstruction to the Virtual Metabolic Human (https://vmh.life) reaction and metabolite nomenclature. The reaction and metabolite database with VMH identifiers as well as the translation table from KBase/Model SEED to VMH reaction and metabolite identiers are retrieved from the folder cobratoolbox/papers/2018_microbiomeModelingToolbox/database. Note that there will likely be reactions and metabolites that are not yet included in the translation table and will thus be missing from the translated model.

USAGE:

[translatedModel, notInTableRxns, notInTableMets] = translateKBaseModel2VMHModel (model, biomassReaction, database)

INPUTS:

  • model – COBRA model structure derived from KBase/ModelSEED, with fields:

    • .rxns - Reaction identifiers

    • .mets - Metabolite identifiers

    • .S - Stoichiometric matrix

    • .genes - Gene identifiers

    • .geneNames - Gene names (optional; propagated to the translated model if present)

    • .grRules - Readable gene protein reaction rules

    • .rxnConfidenceScores - Reaction confidence scores

    • .metNames - Metabolite names

    • .metFormulas - Elemental formulas

    • .metCharges - Metabolite charges

  • biomassReaction – Biomass reaction abbreviation

  • database – Structure containing the reaction and metabolite database, with fields:

    • .reactions - cell array of reaction data (abbreviation, name, reaction formula, …)

    • .metabolites - cell array of metabolite data (abbreviation, name, formula, charge, …)

OUTPUTS:

  • translatedModel – Translated COBRA model structure

  • notInTableRxns – Reactions that are currently not in the translation table

  • notInTableMets – Metabolites that are currently not in the translation table

uptakeMetaboliteGapfill(model, microbeID, database, inputDataFolder)[source]

This function adds exchange, transport and biosynthesis reactions for experimentally shown consumed metabolites according to data collected for the DEMETER pipeline.

USAGE:

[model, uptakeRxnsAdded] = uptakeMetaboliteGapfill (model, microbeID, database, inputDataFolder)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers, used to determine which uptake reactions are already present

  • microbeID – ID of the reconstructed microbe that serves as the reconstruction name and to identify it in input tables

  • database – rBioNet reaction database with fields:

    • .reactions - Cell array with reaction abbreviation (column 1), name (column 2), and formula (column 3)

  • inputDataFolder – Folder with input tables with experimental data and databases that inform the refinement process

OUTPUTS:

  • model – COBRA model structure with added pathways if applies

  • uptakeRxnsAdded – Reactions added based on experimental data