Properties

computeFluxConsistentReactionPresence(modelFolder, propertiesFolder, reconVersion)

This function extracts the presence of flux consistent reactions for a resource of reconstructions that were refined through the semi-automatic refinement pipeline (1 = present in the flux consistent submodel, 0 = not present in the flux consistent submodel).

USAGE:

computeFluxConsistentReactionPresence (modelFolder, propertiesFolder, reconVersion)

INPUTS:

• modelFolder – Folder with COBRA models to be analyzed

• propertiesFolder – Folder where the retrieved reaction presences will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource

computeInternalMetaboliteProduction(modelFolder, propertiesFolder, reconVersion, metList, numWorkers)

This function extracts all metabolites that could be produced internally by at least one refined reconstruction in the tested reconstruction resource. Disregards whether the metabolite can be transported.

USAGE:

computeInternalMetaboliteProduction (modelFolder, propertiesFolder, reconVersion, metList, numWorkers)

INPUTS:

• modelFolder – Folder with reconstructions to be analyzed

• propertiesFolder – Folder where the retrieved uptake and secretion potential will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource (default: “Reconstructions”)

• metList – List of VMH IDs of metabolites to analyze (default: all metabolites in reconstruction resource)

• numWorkers – Number of workers in parallel pool (default: 0)

computeMetabolicDistance(propertiesFolder, reconVersion, numWorkers)

This function computes the Jaccard distance for each pairwise combination of analysed strains in terms of reaction presence and metabolite uptake and secretion potential.

USAGE:

computeMetabolicDistance (propertiesFolder, reconVersion, numWorkers)

INPUTS:

• propertiesFolder – Folder where the reaction presences and uptake/secretion potentials to be analysed are stored

• reconVersion – Name assigned to the reconstruction resource

• numWorkers – Number of workers in parallel pool

computeModelProperties(refinedFolder, infoFilePath, reconVersion, varargin)

Part of the DEMETER pipeline. This function analyzes and plots various properties of the refined and optionally the draft reconstructions. Note that this may be time-consuming.

USAGE:

propertiesFolder = computeModelProperties (refinedFolder, infoFilePath, reconVersion, varargin)

INPUTS:

• refinedFolder – Folder with refined COBRA models to analyze

• infoFilePath – File with information on reconstructions to refine

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

OPTIONAL INPUTS:

• propertiesFolder – Folder where the computed model properties will be stored (default: [pwd filesep ‘modelProperties’])

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

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

• customFeatures – Features other than taxonomy to cluster microbes by. Need to be a table header in the file with information on reconstructions.

OUTPUTS:

propertiesFolder – Folder where the computed model properties were stored

computeReconstructionFeatures(translDraftsFolder, refinedFolder, propertiesFolder, reconVersion, numWorkers)

This function prints a comparison of basic reconstruction features of the draft and refined reconstructions for the refined reconstruction resource.

USAGE:

computeReconstructionFeatures (translDraftsFolder, refinedFolder, propertiesFolder, reconVersion, numWorkers)

INPUTS:

• translDraftsFolder – Folder with translated draft reconstructions

• refinedFolder – Folder with refined reconstructions to be analyzed

• propertiesFolder – Folder where the computed stochiometric and flux consistencies will be stored

• reconVersion – Name assigned to the reconstruction resource

• numWorkers – Number of workers in parallel pool

computeUptakeSecretion(modelFolder, propertiesFolder, reconVersion, metList, numWorkers)

This function extracts all metabolites that could be consumed or secreted by at least one refined reconstruction in the tested reconstruction resource.

USAGE:

computeUptakeSecretion (modelFolder, propertiesFolder, reconVersion, metList, numWorkers)

INPUTS:

• modelFolder – Folder with reconstructions to be analyzed

• propertiesFolder – Folder where the retrieved uptake and secretion potential will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource

• metList – List of VMH IDs of metabolites to analyze (default: all metabolites in reconstruction resource)

• numWorkers – Number of workers in parallel pool (default: 0)

extractReconstructionResourceSubset(modelFolder, infoFilePath, subHeader, subFeature, subsetFolder)

Extracts a subset of a reconstruction resource (e.g., AGORA) that shares a certain feature (e.g., belonging to a particular taxon. Requires providing a table containing the information based on which the subset should be extracted.

USAGE:

[extractedSubset, subsetFolder] = extractReconstructionResourceSubset (modelFolder, infoFilePath, subHeader, subFeature, subsetFolder)

INPUTS:

• modelFolder – Path to folder with reconstruction resource from which the subset should be retrieved

• infoFilePath – Path to text or spreadsheet file with information on each reconstruction in the resource (e.g., ‘AGORA_infoFile.xslx’)

• subHeader – Name of column header in the information table which contains the feature by which the subset should be extracted (e.g., ‘Phylum’)

• subFeature – Name of the feature by which the subset should be extracted (e.g., ‘Bacteroidetes’)

OPTIONAL INPUTS:

subsetFolder – Path to folder in which the subset of reconstructions should be saved (Default: ‘extractedModels’)

OUTPUTS:

• extractedSubset – List of IDs of reconstructions in the extracted subset

• subsetFolder – Path to folder in which the subset of reconstructions is located

getReactionMetabolitePresence(modelFolder, propertiesFolder, reconVersion, numWorkers)

This function extracts the presence of reactions and metabolites for a resource of reconstructions that were refined through the semi-automatic refinement pipeline (1 = present, 0 = not present).

USAGE:

getReactionMetabolitePresence (modelFolder, propertiesFolder, reconVersion, numWorkers)

INPUTS:

• modelFolder – Folder with COBRA models to be analyzed

• propertiesFolder – Folder where the retrieved reaction presences will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource

• numWorkers – Number of workers in parallel pool

getSubsystemPresence(propertiesFolder, reconVersion)

This function extracts the presence of subsystems for a resource of reconstructions that were refined through the semi-automatic refinement pipeline. Shown is the fraction of total reactions in each subsystem for each reconstruction in the resource. Requires the function getreactionPresenceOnTaxonLevels to be run first.

USAGE:

getSubsystemPresence (propertiesFolder, reconVersion)

INPUTS:

• propertiesFolder – Folder where the retrieved subsystem presences will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource

plotMetaboliteProducersConsumers(propertiesFolder, infoFilePath, reconVersion, varargin)

This function creates plots of strains that can consume or secrete a given list of metabolites. Plots are created on the strain level (each reconstruction separately) and, if taxonomical information is provided, on the species, genus, family, order, class, and phylum level.

USAGE:

plotMetaboliteProducersConsumers (propertiesFolder, infoFilePath, reconVersion, varargin)

INPUTS:

• propertiesFolder – Folder where computed uptake and secretion profiles are stored

• infoFilePath – Path to spreadsheet with taxonomical information of the refined strains

• reconVersion – Name assigned to the reconstruction resource

OPTIONAL INPUTS:

• metsToAnalyze – Table with list of metabolites that should be analyzed (default: all computed metabolites)

• metCategory – Name for type of metabolites to analyze that should be in the plots (Default: ‘Metabolites’)

predictGrowthRequirements(model)

Predicts growth requirements for a genome-scale reconstruction. The list of predicted essential exchanges as well as a model constrained with these exchanges are returned.

USAGE:

[growthOnMinimalMedium, essentialExchanges, modelPruned] = predictGrowthRequirements (model)

INPUTS:

model – COBRA model structure with fields:

• .rxns - Reaction identifiers

• .lb - Lower bounds on reaction fluxes

OUTPUTS:

• growthOnMinimalMedium – Bool if growth on defined medium yes or no

• essentialExchanges – Exchanges that need to be open to enable growth

• modelPruned – Model constrained with predicted essential exchanges

printReconstructionContent(modelFolder, propertiesFolder, reconVersion, numWorkers)

This function creates text files containing all reactions and metabolites in the reconstruction resource.

USAGE:

printReconstructionContent (modelFolder, propertiesFolder, reconVersion, numWorkers)

INPUTS:

• modelFolder – Folder with reconstructions to be printed

• propertiesFolder – Folder where the computed stochiometric and flux consistencies will be stored

• reconVersion – Name assigned to the reconstruction resource

• numWorkers – Number of workers in parallel pool

producetSNEPlots(propertiesFolder, infoFilePath, reconVersion, customFeatures)

This function plots reaction presence and uptake and secretion potential by taxon with t-SNE.

USAGE:

producetSNEPlots (propertiesFolder, infoFilePath, reconVersion, customFeatures)

INPUTS:

• propertiesFolder – Folder where the reaction presences and uptake and secretion potential to be analyzed are stored (default: current folder)

• infoFilePath – Path to spreadsheet with taxonomical information of the refined strains

• reconVersion – Name assigned to the reconstruction resource

OPTIONAL INPUTS:

customFeatures – Features other than taxonomy to cluster microbes by. Need to be a table header in the file with information on reconstructions.

rankFeaturesByIncidence(propertiesFolder, reconVersion)

This function counts the incidence of a number of features in the refined reconstruction resource and ranks them from most to least common.

USAGE:

rankFeaturesByIncidence (propertiesFolder, reconVersion)

INPUTS:

• propertiesFolder – Folder where the analyzed features are stored and the results will be stored (default: current folder)

• reconVersion – Name assigned to the reconstruction resource

summarizeFeaturesOnTaxonLevels(propertiesFolder, infoFilePath, reconVersion, customFeatures)

This function summarizes calculated features of the reconstruction resource, if taxonomical information is provided, on the species, genus, family, order, class, and phylum level. A custom feature (.e.g, gram status, source of the strains) can also be used to summarize the data. In this case, the spreadsheet with strain information needs to contain a column with this information.

USAGE:

summarizeFeaturesOnTaxonLevels (propertiesFolder, infoFilePath, reconVersion, customFeatures)

INPUTS:

• propertiesFolder – Folder where the retrieved reaction presences will be stored (default: current folder)

• infoFilePath – Path to spreadsheet with taxonomical information of the refined strains

• reconVersion – Name assigned to the reconstruction resource

OPTIONAL INPUTS:

customFeatures – Features other than taxonomy to cluster microbes by. Need to be a table header in the file with information on reconstructions.