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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.