FROG files¶

In the following the four created reference files and the metadata file are described and examples provided for the e_coli_core.xml model. All output files are tab separated files (TSV) with the first three columns being model, objective, and status. The column model encodes the SBML model id. The column objective encodes the SBML objective id, which is the objective which was optimized in the respective simulation. The column status encodes the status of the simulation. The status can be either optimal (optimization worked) or infeasible (no solution found or problem in simulation).

Metadata file¶

A required metadata file metadata.json encodes information about the curation run and the used software and library. The information is documented at the JSON schema frog-schema-version-1.json <https://raw.githubusercontent.com/matthiaskoenig/fbc_curation/develop/src/fbc_curation/resources/schema/frog-schema-version-1.json>__

The following fields are required:

software.name (required): software used to create the reference files,
software.version (required): software version
model.location (required): SBML model filename
solver.name (required): solver used for optimization,
solver.version (required): solver version

A concrete example of the metadata is shown below

{
  "model_location": "./e_coli_core.xml",
  "model_md5": "4574760460afe9e1b3388dc15f354706",
  "frog_id": "cobrapy_tsv",
  "frog_software": {
    "name": "fbc_curation",
    "version": "0.2.2",
    "url": "https://doi.org/10.5281/zenodo.3708271"
  },
  "curators": [],
  "software": {
    "name": "cobrapy",
    "version": "0.26.0",
    "url": "https://github.com/opencobra/cobrapy"
  },
  "solver": {
    "name": "glpk",
    "version": "5.0",
    "url": null
  },
  "environment": "posix, Linux, 5.15.0-53-generic"
}

See e_coli_core/metadata.json.

01 Objective value¶

The objective value file 01_objective.tsv contains the four columns with the headers model, objective, status, and value. The model column stores the SBML model filename. The value is the optimal value of the respective objective function when the model is optimized. If the status is infeasible, no value is provided, i.e., the value is empty.

model	objective	status	value
./e_coli_core.xml	obj	optimal	0.8739215069684295

For an example file see e_coli_core/01_objective.tsv. For more information on how to simulate the FBA see https://cobrapy.readthedocs.io/en/latest/simulating.html.

02 Flux variability analysis (FVA)¶

The FVA file 02_fva.tsv contains six columns with the headers model, objective, reaction, flux, status, minimum and maximum. The model column stores the SBML model filename. The reaction column stores the SBML reaction id. The minimum and maximum columns contain the minimum and maximum values of the FVA. The rows are sorted based on the SBML reaction identifier. The status contains the status of the optimization (optimal or infeasible). If the status is infeasible the value is empty. Flux variability is calculated with fraction_optimum = 1.0, i.e. the objective of the model is set to its maximum in secondary optimization (percent of optimum is 100%). The flux column stores the reference flux through the objective reaction which is objective_value * fraction_optimum. In case of fraction_optimum = 1.0 this is identical to the value in `01_objective.tsv

model	objective	reaction	flux	status	minimum	maximum	fraction_optimum
./e_coli_core.xml	obj	R_ACALD	0.8739215069684295	optimal	1.1348525979450152e-14	0.0	1.0
./e_coli_core.xml	obj	R_ACALDt	0.8739215069684295	optimal	3.662182303830574e-15	0.0	1.0
./e_coli_core.xml	obj	R_ACKr	0.8739215069684295	optimal	0.0	0.0	1.0
./e_coli_core.xml	obj	R_ACONTa	0.8739215069684295	optimal	6.007249575350388	6.007249575350355	1.0
./e_coli_core.xml	obj	R_ACONTb	0.8739215069684295	optimal	6.007249575350388	6.007249575350264	1.0
./e_coli_core.xml	obj	R_ACt2r	0.8739215069684295	optimal	1.772023695401875e-14	0.0	1.0
./e_coli_core.xml	obj	R_ADK1	0.8739215069684295	optimal	0.0	-3.4583850794047745e-14	1.0
./e_coli_core.xml	obj	R_AKGDH	0.8739215069684295	optimal	5.064375661482467	5.0643756614820665	1.0
./e_coli_core.xml	obj	R_AKGt2r	0.8739215069684295	optimal	0.0	0.0	1.0
./e_coli_core.xml	obj	R_ALCD2x	0.8739215069684295	optimal	9.884200046617872e-15	0.0	1.0
./e_coli_core.xml	obj	R_ATPM	0.8739215069684295	optimal	8.39	8.389999999999924	1.0
./e_coli_core.xml	obj	R_ATPS4r	0.8739215069684295	optimal	45.51400977451763	45.514009774517376	1.0
./e_coli_core.xml	obj	R_BIOMASS_Ecoli_core_w_GAM	0.8739215069684295	optimal	0.873921506968431	0.8739215069684305	1.0
./e_coli_core.xml	obj	R_CO2t	0.8739215069684295	optimal	-22.80983331020497	-22.80983331020505	1.0
...

See for instance: e_coli_core/02_fva.tsv. For more information: https://cobrapy.readthedocs.io/en/latest/simulating.html#Running-FVA

03 Gene deletions¶

The gene deletion file 03_gene_deletion.tsv contains five columns with the headers model, objective, gene, status and value. The model column stores the SBML model filename. The gene column contains the SBML gene identifiers. The status and value columns contain the status of the optimization (optimal or infeasible) and optimal value under the given gene deletion. If the status is infeasible the value is empty. The rows are sorted based on gene identifier.

model	objective	gene	status	value
./e_coli_core.xml	obj	G_b0008	optimal	0.873921506968431
./e_coli_core.xml	obj	G_b0114	optimal	0.7966959254309566
./e_coli_core.xml	obj	G_b0115	optimal	0.7966959254309566
./e_coli_core.xml	obj	G_b0116	optimal	0.7823510529477393
./e_coli_core.xml	obj	G_b0118	optimal	0.8739215069684314
./e_coli_core.xml	obj	G_b0351	optimal	0.8739215069684306
./e_coli_core.xml	obj	G_b0356	optimal	0.873921506968431
...
./e_coli_core.xml	obj	G_b2415	infeasible	NaN
./e_coli_core.xml	obj	G_b2416	infeasible	NaN
...

See for instance: e_coli_core/03_gene_deletion.tsv. For more information: https://cobrapy.readthedocs.io/en/latest/deletions.html

04 Reaction deletions¶

The reaction deletion file 04_reaction_deletion.tsv contains five columns with the headers model, objective, reaction, status and value. The model column stores the SBML model filename. The reaction column contains the SBML reaction identifiers. The status and value columns contain the status of the optimization (optimal or infeasible) and optimal value under the given reaction deletion. If the status is infeasible the value is empty. The rows are sorted based on reaction identifier.

model	objective	reaction	status	value
./e_coli_core.xml	obj	R_ACALD	optimal	0.873921506968431
./e_coli_core.xml	obj	R_ACALDt	optimal	0.873921506968431
./e_coli_core.xml	obj	R_ACKr	optimal	0.8739215069684305
./e_coli_core.xml	obj	R_ACONTa	optimal	-3.2790312837402413e-15
./e_coli_core.xml	obj	R_ACONTb	optimal	-4.655434573658402e-15
./e_coli_core.xml	obj	R_ACt2r	optimal	0.8739215069684313
./e_coli_core.xml	obj	R_ADK1	optimal	0.873921506968431
./e_coli_core.xml	obj	R_AKGDH	optimal	0.8583074080226888
...

See for instance: e_coli_core/04_reaction_deletion.tsv. For more information: https://cobrapy.readthedocs.io/en/latest/deletions.html.