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https://github.com/matthiaskoenig/fbc_curation
FROG analysis in python for the reproducibility of FBC models
https://github.com/matthiaskoenig/fbc_curation
fbc fva sbml
Last synced: 3 months ago
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FROG analysis in python for the reproducibility of FBC models
- Host: GitHub
- URL: https://github.com/matthiaskoenig/fbc_curation
- Owner: matthiaskoenig
- License: lgpl-3.0
- Created: 2020-03-12T13:39:07.000Z (almost 5 years ago)
- Default Branch: develop
- Last Pushed: 2023-03-26T20:16:36.000Z (almost 2 years ago)
- Last Synced: 2024-07-08T23:21:47.152Z (7 months ago)
- Topics: fbc, fva, sbml
- Language: Python
- Homepage: https://runfrog.de
- Size: 19 MB
- Stars: 8
- Watchers: 5
- Forks: 3
- Open Issues: 20
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
.. image:: https://raw.githubusercontent.com/matthiaskoenig/fbc_curation/develop/docs/images/icon/frog_icon_mirror-100x80-300dpi.png
:align: left
:alt: FROG logo
fbc_curation: FROG analysis in Python
=====================================
.. image:: https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg
:target: https://github.com/matthiaskoenig/fbc_curation/workflows/CI-CD
:alt: GitHub Actions CI/CD Status
.. image:: https://img.shields.io/pypi/v/fbc-curation.svg
:target: https://pypi.org/project/fbc_curation/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/fbc-curation.svg
:target: https://pypi.org/project/fbc_curation/
:alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/fbc-curation.svg
:target: http://opensource.org/licenses/LGPL-3.0
:alt: GNU Lesser General Public License 3
.. image:: https://readthedocs.org/projects/fbc_curation/badge/?version=latest
:target: https://fbc-curation.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://codecov.io/gh/matthiaskoenig/fbc_curation/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/matthiaskoenig/fbc_curation
:alt: Codecov
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg
:target: https://doi.org/10.5281/zenodo.3708271
:alt: Zenodo DOI
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/ambv/black
:alt: Black
The project :code:`fbc_curation` implements the FROG analysis for reproducibility of constraint-based models in Python.
FROG can be run
* programmatically in python
* using the :code:`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
.. image:: https://img.shields.io/pypi/pyversions/fbc-curation.svg
:target: https://pypi.org/project/fbc_curation/
:alt: Supported Python Versions
:code:`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 :code:`fbc_curation` or :code:`runfrog` please cite us via
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg
:target: https://doi.org/10.5281/zenodo.3597770
:alt: Zenodo DOI
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 :code:`runfrog` command line tool
.. code:: bash
$ 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
.. code:: python
from fbc_curation.worker import run_frog
run_frog(model_path, omex_path)
Here a complete example with comparison of the FROG results
.. code:: python
"""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
.. code:: bash
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