Files in the data folder#

Every file a project's data folder can hold, and where each one gets used or produced. File formats (TSV, JSON) are the same in both languages, so a data folder built with one toolbox can be reused with the other; see Getting started for the folder layout this table assumes.

File

Description

Used in

ComplexPortal.json

Enzyme complex information retrieved from the Complex Portal, downloaded by getComplexData (Python: get_complex_data).

Building an empty ecModel

customKcats.tsv

Manually curated kcat values for specific enzymes or reactions, constructed by the user from other data sources.

Applying kcats

DLKcat.tsv

Input and, once run, output for DLKcat kcat prediction. Generated by writeDLKcatInput (Python: write_dlkcat_input).

Gathering kcats

fluxData.tsv

Experimental growth rate, protein content and carbon-source uptake, used to constrain the ecModel during proteomics integration and in flux-variability comparisons. Exchange fluxes in mmol/gDCWh; uptake negative, excretion positive. Not required for the initial reconstruction.

Proteomics integration, Simulation and analysis

kegg.tsv

KEGG information for the organism: UniProt protein ID, gene, KEGG gene ID, EC number, MW, pathway and sequence. Downloaded by loadDatabases (Python: geckopy kegg-download).

Getting started, Gathering kcats

paxDB.tsv

Protein abundance data used to compute the f factor (the mass fraction of proteins accounted for in the ecModel). Retrieved from pax-db.org. Without it, f defaults to 0.5.

Applying kcats

proteomics.tsv

Measured protein levels (mg protein/gDCW) from one or more experiments: UniProt identifiers in the first column, protein levels from individual replicates in each subsequent column.

Proteomics integration

smilesDB.tsv

SMILES for the metabolites of the ecModel, generated when findMetSmiles (Python: find_met_smiles) queries PubChem.

Gathering kcats

uniprot.tsv

UniProt data for the organism: protein identifier, gene identifier, EC number, MW and sequence. Downloaded by loadDatabases (Python: geckopy uniprot-download).

Getting started, Building an empty ecModel

uniprotConversion.tsv

Conversion table needed when no UniProt field carries genes in the same format as the ecModel's gene identifiers. First column is the ecModel's gene identifiers, second is the UniProt identifier. Constructed by the user.

Getting started

See also#

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