fbc-curation 0.2.3

FBC reference files for SBML model curation.

fbc_curation: FROG analysis in Python

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 runfrog command 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 the model behavior, e.g., when submitting the model to BioModels. The latest version supports

fbc_curation provides two implementations of FROG using

• cobrapy based on COBRApy (Constraint-Based Reconstruction and Analysis in Python)

• cameo cameo based on Cameo (Computer Aided Metabolic Engineering and Optimization)

For more information see the following resources

• Documentation: https://fbc-curation.readthedocs.io

• 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

• FROG BioModels submission: https://www.ebi.ac.uk/biomodels/curation/fbc.

If you have any questions or issues please open an issue.

How to cite

If you use fbc_curation or runfrog please cite us via

Installation

fbc_curation is available from pypi and can be installed via:

pip install fbc-curation

The latest develop version can be installed via:

pip install git+https://github.com/matthiaskoenig/fbc-curation.git@develop

Run FROG

Command line tool

After installation FROG analysis can be performed using the runfrog command line tool

$ runfrog

──────────────────────────────────────────────────────────────────────────────────
🐸 FBC CURATION FROG ANALYSIS 🐸
Version 0.2.1 (https://github.com/matthiaskoenig/fbc_curation)
Citation https://doi.org/10.5281/zenodo.3708271
──────────────────────────────────────────────────────────────────────────────────
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
──────────────────────────────────────────────────────────────────────────────────

Website

FROG can be easily executed via the website https://runfrog.de

REST API

FROG can be execute via the REST API https://runfrog.de/docs

Python

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 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 writes 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",
    )

The typically output of a FROG analysis is depicted 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
───────────────────────────────────────────────────────────────────────────────────────

License

• Source Code: LGPLv3

• Documentation: CC BY-SA 4.0

The fbc_curation source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme 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).

© 2020-2022 Matthias König