Model adapter parameters

The core obj.params entries in the MATLAB model adapter, and the corresponding TOML key in the Python model_adapter.toml (dotted keys are [section] tables). Example values come from the full_ecModel tutorial; see Getting started for the model adapter itself.

This table covers the parameters used across the main reconstruction workflow. It omits two specialized groups: the CMA-ES kcat-tuning hyperparameters (obj.params.evotune.* in MATLAB, EvotuneParams in Python's adapter.params, covered by Growth-rate tuning) and, Python-only, OkpParams for OpenKineticsPredictor settings and the kcat_aggregate_brenda / kcat_aggregate_candidates / kcat_aggregate_isozymes defaults that let an adapter centrally override a kcat-matching function's aggregation choice.

MATLAB parameter	Python (TOML)	Example	Explanation
bioRxn	bio_rxn	r_4041	Reaction identifier for the biomass or growth pseudo-reaction, whose flux is the growth rate in h^-1.
c_source	c_source	r_1714	Reaction identifier for the glucose exchange reaction (or other preferred carbon source).
complex.taxonomicID	complex.taxonomic_id	559292	Taxonomic identifier as available from the Complex Portal.
convGEM	conv_gem	fullfile(obj.params.path, 'models', 'yeast-GEM.xml') (MATLAB) / "models/yeast-GEM.yml" (Python)	Path to the starting conventional GEM file.
enzyme_comp	enzyme_comp	cytoplasm	Compartment name in which added enzymes are located; must match one of the ecModel's compartment names.
f	f	0.5	Fraction of enzymes in the ecModel relative to all proteins (g enzyme/g protein). calculateFfactor() (Python: calculate_f_factor) computes it from a proteomics dataset.
gR_exp	gr_exp	0.41	Reference (experimentally observed) maximum growth rate in h^-1, the default tuning target in Growth-rate tuning.
kegg.geneID	kegg.gene_id	kegg	The gene identifier or database link from KEGG that corresponds to the ecModel genes; for human-GEM this is Ensembl.
kegg.ID	kegg.id	sce	Organism ID in the KEGG database, from the KEGG organism list.
org_name	org_name	saccharomyces cerevisiae	Scientific name of the organism, used by fuzzyKcatMatching (Python: fuzzy_kcat_matching).
path	path	fullfile(findGECKOroot, 'tutorials', 'full_ecModel') (MATLAB)	Path to the directory holding all ecModel-specific content. In Python, path is set automatically to the folder passed to ModelAdapter.from_folder(), not written in the TOML file itself.
Ptot	p_tot	0.5	Total protein content in the cell (g protein/gDCW).
sigma	sigma	0.5	Average enzyme saturation factor sigma.
uniprot.geneIDfield	uniprot.gene_id_field	gene_oln	UniProt field with the gene identifiers used in the ecModel. Must be one of the "Returned Field" entries under "Names & Taxonomy".
uniprot.ID	uniprot.id	UP000002311	Identifier of the UniProt dataset (by taxonomy or proteome) with complete coverage of the ecModel genes.
uniprot.type	uniprot.type	proteome	Whether uniprot.ID is a taxonomy or a proteome identifier.
uniprot.reviewed	uniprot.reviewed	true	Whether only reviewed UniProt data is considered. Reviewed data has the highest confidence but may have low coverage for nonmodel organisms.

See also

• Getting started, where the model adapter is created and populated.

• Files in the data folder, the other project-wide reference table.