{"id":19221671,"url":"https://github.com/matthiaskoenig/fbc_curation","last_synced_at":"2025-10-19T04:42:33.167Z","repository":{"id":39992064,"uuid":"246843794","full_name":"matthiaskoenig/fbc_curation","owner":"matthiaskoenig","description":"FROG analysis in python for the reproducibility of FBC 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image:: https://raw.githubusercontent.com/matthiaskoenig/fbc_curation/develop/docs/images/icon/frog_icon_mirror-100x80-300dpi.png\n   :align: left\n   :alt: FROG logo\n\nfbc_curation: FROG analysis in Python\n=====================================\n\n.. image:: https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg\n   :target: https://github.com/matthiaskoenig/fbc_curation/workflows/CI-CD\n   :alt: GitHub Actions CI/CD Status\n\n.. image:: https://img.shields.io/pypi/v/fbc-curation.svg\n   :target: https://pypi.org/project/fbc_curation/\n   :alt: Current PyPI Version\n\n.. image:: https://img.shields.io/pypi/pyversions/fbc-curation.svg\n   :target: https://pypi.org/project/fbc_curation/\n   :alt: Supported Python Versions\n\n.. image:: https://img.shields.io/pypi/l/fbc-curation.svg\n   :target: http://opensource.org/licenses/LGPL-3.0\n   :alt: GNU Lesser General Public License 3\n\n.. image:: https://readthedocs.org/projects/fbc_curation/badge/?version=latest\n   :target: https://fbc-curation.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n.. image:: https://codecov.io/gh/matthiaskoenig/fbc_curation/branch/develop/graph/badge.svg\n   :target: https://codecov.io/gh/matthiaskoenig/fbc_curation\n   :alt: Codecov\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg\n   :target: https://doi.org/10.5281/zenodo.3708271\n   :alt: Zenodo DOI\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/ambv/black\n   :alt: Black\n\n\nThe project :code:`fbc_curation` implements the FROG analysis for reproducibility of constraint-based models in Python.\nFROG can be run \n\n* programmatically in python\n* using the :code:`runfrog` command line tool available in this package\n* via the website `https://runfrog.de \u003chttps://runfrog.de\u003e`__\n* via the REST API `https://runfrog.de/docs \u003chttps://runfrog.de/docs\u003e`__\n\nThe FROG analysis creates standardized reference files for a given constraint-based computational model. \nThe FROG files can be used in the model curation process for validating the model behavior, e.g., when\nsubmitting the model to `BioModels \u003chttps://www.ebi.ac.uk/biomodels/curation/fbc\u003e`__. \nThe latest version supports \n\n.. image:: https://img.shields.io/pypi/pyversions/fbc-curation.svg\n   :target: https://pypi.org/project/fbc_curation/\n   :alt: Supported Python Versions\n\n:code:`fbc_curation` provides two implementations of FROG using\n\n* `cobrapy \u003chttps://github.com/opencobra/cobrapy\u003e`__ based on COBRApy (Constraint-Based Reconstruction and Analysis in Python)\n* `cameo \u003chttps://github.com/biosustain/cameo\u003e`__ cameo based on Cameo (Computer Aided Metabolic Engineering and Optimization)\n\nFor more information see the following resources\n\n* **Documentation**: `https://fbc-curation.readthedocs.io \u003chttps://fbc-curation.readthedocs.io\u003e`__\n* **Website**: `https://runfrog.de \u003chttps://runfrog.de\u003e`__\n* **REST API**: `https://runfrog.de/docs \u003chttps://runfrog.de/docs\u003e`__\n* **FROG format**: `FROG version 1 \u003chttps://fbc-curation.readthedocs.io/en/latest/reference_files.html\u003e`__\n* **FROG JSON schema**: `frog-schema-version-1.json \u003chttps://raw.githubusercontent.com/matthiaskoenig/fbc_curation/develop/src/fbc_curation/resources/schema/frog-schema-version-1.json\u003e`__.\n* **Code**: `https://github.com/matthiaskoenig/fbc_curation \u003chttps://github.com/matthiaskoenig/fbc_curation\u003e`_\n* **FROG BioModels submission**: `https://www.ebi.ac.uk/biomodels/curation/fbc \u003chttps://www.ebi.ac.uk/biomodels/curation/fbc\u003e`__.\n\nIf you have any questions or issues please `open an issue \u003chttps://github.com/matthiaskoenig/fbc_curation/issues\u003e`__. \n\nHow to cite\n===========\nIf you use :code:`fbc_curation` or :code:`runfrog` please cite us via\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg\n   :target: https://doi.org/10.5281/zenodo.3597770\n   :alt: Zenodo DOI\n\nInstallation\n============\n``fbc_curation`` is available from `pypi \u003chttps://pypi.python.org/pypi/fbc-curation\u003e`__ and\ncan be installed via::\n\n    pip install fbc-curation\n\nThe latest develop version can be installed via::\n\n    pip install git+https://github.com/matthiaskoenig/fbc-curation.git@develop\n\n\nRun FROG\n========\n\nCommand line tool\n-----------------\n\nAfter installation FROG analysis can be performed using the :code:`runfrog` command line tool\n\n.. code:: bash\n\n    $ runfrog\n    \n    ──────────────────────────────────────────────────────────────────────────────────\n    🐸 FBC CURATION FROG ANALYSIS 🐸\n    Version 0.2.1 (https://github.com/matthiaskoenig/fbc_curation)\n    Citation https://doi.org/10.5281/zenodo.3708271\n    ──────────────────────────────────────────────────────────────────────────────────\n    Usage: runfrog [options]\n    \n    Options:\n      -h, --help            show this help message and exit\n      -i INPUT_PATH, --input=INPUT_PATH\n                            (required) path to COMBINE archive (OMEX) with SBML\n                            model or an SBML model\n      -o OUTPUT_PATH, --output=OUTPUT_PATH\n                            (required) omex output path to write FROG\n    ──────────────────────────────────────────────────────────────────────────────────\n\nWebsite\n-------\nFROG can be easily executed via the website `https://runfrog.de \u003chttps://runfrog.de\u003e`__\n\nREST API\n--------\nFROG can be execute via the REST API `https://runfrog.de/docs \u003chttps://runfrog.de/docs\u003e`__\n\nPython\n------\nTo run FROG programmatically via python use the `run_frog` function\n\n\n.. code:: python\n\n    from fbc_curation.worker import run_frog\n    \n    run_frog(model_path, omex_path)\n\n\nHere a complete example with comparison of the FROG results\n\n.. code:: python\n\n    \"\"\"FROG example using `fbc_curation`.\"\"\"\n    from pathlib import Path\n    \n    from fbc_curation.compare import FrogComparison\n    from fbc_curation.worker import run_frog\n    \n    \n    def create_frog(model_path: Path, omex_path: Path) -\u003e None:\n        \"\"\"Create FROG report and writes OMEX for given model.\"\"\"\n    \n        # create FROG and write to COMBINE archive\n        run_frog(\n            source_path=model_path,\n            omex_path=omex_path,\n        )\n    \n        # compare FROG results in created COMBINE archive\n        model_reports = FrogComparison.read_reports_from_omex(omex_path=omex_path)\n        for _, reports in model_reports.items():\n            FrogComparison.compare_reports(reports=reports)\n    \n    \n    if __name__ == \"__main__\":\n        base_path = Path(\".\")\n        create_frog(\n            model_path=base_path / \"e_coli_core.xml\",\n            omex_path=base_path / \"e_coli_core_FROG.omex\",\n        )\n\nThe typically output of a FROG analysis is depicted below\n\n.. code:: bash\n\n    runfrog -i e_coli_core.xml -o e_coli_core.omex\n\n    ───────────────────────────────────────────────────────────────────────────────────────\n    🐸 FBC CURATION FROG ANALYSIS 🐸\n    Version 0.2.3 (https://github.com/matthiaskoenig/fbc_curation)\n    Citation https://doi.org/10.5281/zenodo.3708271\n    ───────────────────────────────────────────────────────────────────────────────────────\n    INFO     Loading 'e_coli_core.xml'                                         worker.py:70\n    WARNING  Omex path 'e_coli_core.xml' is not a zip archive.                  omex.py:500\n    ───────────────────────────────── FROG CuratorCobrapy ─────────────────────────────────\n    INFO     * metadata                                                      curator.py:107\n    INFO     * objectives                                                    curator.py:110\n    INFO     * fva                                                           curator.py:113\n    INFO     * reactiondeletions                                             curator.py:116\n    INFO     * genedeletions                                                 curator.py:119\n    INFO     FROG created in '0.977' [s]                                      worker.py:178\n    ────────────────────────────────── FROG CuratorCameo ──────────────────────────────────\n    INFO     * metadata                                                      curator.py:107\n    INFO     * objectives                                                    curator.py:110\n    INFO     * fva                                                           curator.py:113\n    INFO     * reactiondeletions                                             curator.py:116\n    INFO     * genedeletions                                                 curator.py:119\n    INFO     FROG created in '1.219' [s]                                      worker.py:178\n    ───────────────────────────────────── Write OMEX ──────────────────────────────────────\n    WARNING  Existing omex is overwritten: 'e_coli_core.omex'                   omex.py:680\n    INFO     Reports in omex:                                                 compare.py:60\n             {'./e_coli_core.xml': ['cobrapy', 'cobrapy_tsv', 'cameo',                     \n             'cameo_tsv']}                                                                 \n    ────────────────────────────── Comparison of FROGReports ──────────────────────────────\n    --- objective ---\n                 cobrapy  cobrapy_tsv  cameo  cameo_tsv\n    cobrapy            1            1      1          1\n    cobrapy_tsv        1            1      1          1\n    cameo              1            1      1          1\n    cameo_tsv          1            1      1          1\n    --- fva ---\n                 cobrapy  cobrapy_tsv  cameo  cameo_tsv\n    cobrapy            1            1      1          1\n    cobrapy_tsv        1            1      1          1\n    cameo              1            1      1          1\n    cameo_tsv          1            1      1          1\n    --- reaction_deletion ---\n                 cobrapy  cobrapy_tsv  cameo  cameo_tsv\n    cobrapy            1            1      1          1\n    cobrapy_tsv        1            1      1          1\n    cameo              1            1      1          1\n    cameo_tsv          1            1      1          1\n    --- gene_deletion ---\n                 cobrapy  cobrapy_tsv  cameo  cameo_tsv\n    cobrapy            1            1      1          1\n    cobrapy_tsv        1            1      1          1\n    cameo              1            1      1          1\n    cameo_tsv          1            1      1          1\n    ───────────────────────────────────────────────────────────────────────────────────────\n    Equal: True\n    ───────────────────────────────────────────────────────────────────────────────────────\n\n\nLicense\n=======\n\n* Source Code: `LGPLv3 \u003chttp://opensource.org/licenses/LGPL-3.0\u003e`__\n* Documentation: `CC BY-SA 4.0 \u003chttp://creativecommons.org/licenses/by-sa/4.0/\u003e`__\n\nThe ``fbc_curation`` source is released under both the GPL and LGPL licenses version 2 or\nlater. You may choose which license you choose to use the software under.\n\nThis program is free software: you can redistribute it and/or modify it under\nthe terms of the GNU General Public License or the GNU Lesser General Public\nLicense as published by the Free Software Foundation, either version 2 of the\nLicense, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY\nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\nPARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nFunding\n=======\nMatthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)\nwithin the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) \nand by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 \n\"`QuaLiPerF \u003chttps://qualiperf.de\u003e`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - \nA Systems Medicine Approach)\" by grant number 436883643 and by grant number 465194077 \n(Priority Programme SPP 2311, Subproject SimLivA). \n\n© 2020-2022 Matthias König\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthiaskoenig%2Ffbc_curation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatthiaskoenig%2Ffbc_curation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthiaskoenig%2Ffbc_curation/lists"}