The project fbc_curation implements the FROG analysis for reproducibility of constraint-based models in Python. FROG can be run
- programmatically in Python
- using the
runfrogcommand line tool available in this package - via the website https://runfrog.de
- via the REST API https://runfrog.de/docs
The FROG analysis creates standardized reference files for a given constraint-based computational model. The FROG files can be used in the model curation process for validating model behavior, e.g., when submitting the model to BioModels.
fbc_curation provides two implementations of FROG using
cobrapy— Constraint-Based Reconstruction and Analysis in Pythoncameo— Computer Aided Metabolic Engineering and Optimization
For more information see the following resources:
- Documentation: https://matthiaskoenig.github.io/fbc_curation/
- Website: https://runfrog.de
- REST API: https://runfrog.de/docs
- FROG format: FROG version 1
- FROG JSON schema:
frog-schema-version-1.json - Code: https://github.com/matthiaskoenig/fbc_curation
- Code Website: https://github.com/matthiaskoenig/runfrog
- FROG BioModels submission: https://www.ebi.ac.uk/biomodels/curation/fbc
If you have any questions or issues please open an issue.
If you use fbc_curation or runfrog please cite us via
fbc_curation is available from PyPI and can be installed via:
pip install fbc-curationAfter installation, FROG analysis can be performed using the runfrog command line tool:
$ runfrog
──────────────────────────────────────────────────────────────────────────────────
🐸 FBC CURATION FROG ANALYSIS 🐸
Version 0.3.1 (https://github.com/matthiaskoenig/fbc_curation)
Citation https://doi.org/10.5281/zenodo.3708271
──────────────────────────────────────────────────────────────────────────────────
Required argument '--input' missing
Usage: runfrog [options]
Options:
-h, --help show this help message and exit
-i INPUT_PATH, --input=INPUT_PATH
(required) path to COMBINE archive (OMEX) with SBML
model or an SBML model
-o OUTPUT_PATH, --output=OUTPUT_PATH
(required) omex output path to write FROG
──────────────────────────────────────────────────────────────────────────────────FROG can be easily executed via the website https://runfrog.de.
FROG can be executed via the REST API https://runfrog.de/docs.
To run FROG programmatically via Python use the run_frog function:
from fbc_curation.worker import run_frog
run_frog(model_path, omex_path)Here is a complete example with comparison of the FROG results:
"""FROG example using `fbc_curation`."""
from pathlib import Path
from fbc_curation.compare import FrogComparison
from fbc_curation.worker import run_frog
def create_frog(model_path: Path, omex_path: Path) -> None:
"""Create FROG report and write OMEX for given model."""
# create FROG and write to COMBINE archive
run_frog(
source_path=model_path,
omex_path=omex_path,
)
# compare FROG results in created COMBINE archive
model_reports = FrogComparison.read_reports_from_omex(omex_path=omex_path)
for _, reports in model_reports.items():
FrogComparison.compare_reports(reports=reports)
if __name__ == "__main__":
base_path = Path(".")
create_frog(
model_path=base_path / "e_coli_core.xml",
omex_path=base_path / "e_coli_core_FROG.omex",
)Typical output of a FROG analysis is shown below:
runfrog -i e_coli_core.xml -o e_coli_core.omex
───────────────────────────────────────────────────────────────────────────────────────
🐸 FBC CURATION FROG ANALYSIS 🐸
Version 0.2.3 (https://github.com/matthiaskoenig/fbc_curation)
Citation https://doi.org/10.5281/zenodo.3708271
───────────────────────────────────────────────────────────────────────────────────────
INFO Loading 'e_coli_core.xml' worker.py:70
WARNING Omex path 'e_coli_core.xml' is not a zip archive. omex.py:500
───────────────────────────────── FROG CuratorCobrapy ────────────────────────────────
INFO * metadata curator.py:107
INFO * objectives curator.py:110
INFO * fva curator.py:113
INFO * reactiondeletions curator.py:116
INFO * genedeletions curator.py:119
INFO FROG created in '0.977' [s] worker.py:178
────────────────────────────────── FROG CuratorCameo ─────────────────────────────────
INFO * metadata curator.py:107
INFO * objectives curator.py:110
INFO * fva curator.py:113
INFO * reactiondeletions curator.py:116
INFO * genedeletions curator.py:119
INFO FROG created in '1.219' [s] worker.py:178
───────────────────────────────────── Write OMEX ─────────────────────────────────────
WARNING Existing omex is overwritten: 'e_coli_core.omex' omex.py:680
INFO Reports in omex: compare.py:60
{'./e_coli_core.xml': ['cobrapy', 'cobrapy_tsv', 'cameo',
'cameo_tsv']}
────────────────────────────── Comparison of FROGReports ─────────────────────────────
--- objective ---
cobrapy cobrapy_tsv cameo cameo_tsv
cobrapy 1 1 1 1
cobrapy_tsv 1 1 1 1
cameo 1 1 1 1
cameo_tsv 1 1 1 1
--- fva ---
cobrapy cobrapy_tsv cameo cameo_tsv
cobrapy 1 1 1 1
cobrapy_tsv 1 1 1 1
cameo 1 1 1 1
cameo_tsv 1 1 1 1
--- reaction_deletion ---
cobrapy cobrapy_tsv cameo cameo_tsv
cobrapy 1 1 1 1
cobrapy_tsv 1 1 1 1
cameo 1 1 1 1
cameo_tsv 1 1 1 1
--- gene_deletion ---
cobrapy cobrapy_tsv cameo cameo_tsv
cobrapy 1 1 1 1
cobrapy_tsv 1 1 1 1
cameo 1 1 1 1
cameo_tsv 1 1 1 1
───────────────────────────────────────────────────────────────────────────────────────
Equal: True
───────────────────────────────────────────────────────────────────────────────────────- Source Code: MIT
- Documentation: CC BY-SA 4.0
Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
© 2020–2025 Matthias König