{"id":20371790,"url":"https://github.com/biosustain/multitfa","last_synced_at":"2025-04-12T06:25:15.897Z","repository":{"id":53019573,"uuid":"160494933","full_name":"biosustain/multitfa","owner":"biosustain","description":"Multivariate thermodynamics-based metabolic flux analysis in Python.","archived":false,"fork":false,"pushed_at":"2023-12-19T01:52:08.000Z","size":74295,"stargazers_count":9,"open_issues_count":5,"forks_count":2,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-04-06T10:44:49.895Z","etag":null,"topics":["cobrapy","fba","metabolism","multitfa","multivariate","python3","tfa","thermodynamics","tmfa"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biosustain.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.rst","contributing":".github/CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.rst","governance":null,"roadmap":null,"authors":null}},"created_at":"2018-12-05T09:39:17.000Z","updated_at":"2024-12-03T04:30:29.000Z","dependencies_parsed_at":"2024-01-10T21:01:49.340Z","dependency_job_id":"560fe7d6-1175-4bca-b762-0a69ea953250","html_url":"https://github.com/biosustain/multitfa","commit_stats":{"total_commits":234,"total_committers":4,"mean_commits":58.5,"dds":"0.43162393162393164","last_synced_commit":"ab5a9bf6c19a94a221c9a137cccfcacdc2c1cb50"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fmultitfa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fmultitfa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fmultitfa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fmultitfa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosustain","download_url":"https://codeload.github.com/biosustain/multitfa/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248526509,"owners_count":21118919,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cobrapy","fba","metabolism","multitfa","multivariate","python3","tfa","thermodynamics","tmfa"],"created_at":"2024-11-15T01:09:46.391Z","updated_at":"2025-04-12T06:25:15.858Z","avatar_url":"https://github.com/biosustain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"========\nmultiTFA\n========\n\n.. image:: https://img.shields.io/pypi/v/multitfa.svg\n   :target: https://pypi.org/project/multitfa/\n   :alt: Current PyPI Version\n\n.. image:: https://img.shields.io/pypi/pyversions/multitfa.svg\n   :target: https://pypi.org/project/multitfa/\n   :alt: Supported Python Versions\n\n.. image:: https://img.shields.io/pypi/l/multitfa.svg\n   :target: https://www.apache.org/licenses/LICENSE-2.0\n   :alt: Apache Software License Version 2.0\n\n.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg\n   :target: .github/CODE_OF_CONDUCT.md\n   :alt: Code of Conduct\n\n.. image:: https://github.com/biosustain/multitfa/workflows/CI-CD/badge.svg\n   :target: https://github.com/biosustain/multitfa/workflows/CI-CD\n   :alt: GitHub Actions\n\n.. image:: https://codecov.io/gh/biosustain/multitfa/branch/main/graph/badge.svg\n   :target: https://codecov.io/gh/biosustain/multitfa\n   :alt: Codecov\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/ambv/black\n   :alt: Code Style Black\n\n.. image:: https://readthedocs.org/projects/multitfa/badge/?version=latest\n   :target: https://multitfa.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n.. summary-start\n\nWe present multiTFA, a multivariate thermodynamics-based metabolic flux analysis\npackage for Python. The framework takes advantage of the reactions' Gibbs free\nenergy covariance matrix to tightly constrain metabolic models using\nthermodynamic constraints. It represents an improvement over a previous\nthermodynamic metabolic flux analysis (tMFA) method described in [1]_.\n\nThis implementation requires a COBRA model as input, as well as additional\ncompartment conditions and metabolite concentrations. It allows user to perform\nvarious thermodynamic analyses on COBRA models, such as thermodynamic metabolic\nflux analysis, variability analysis, or flux sampling.  Please see below for\nfurther details.\n\n\nInstall\n=======\n\nTo install multitfa from PyPI is as simple as: (We recommend using a `virtual environment \u003chttps://docs.python-guide.org/dev/virtualenvs/\u003e`_).\n\n.. code-block:: console\n\n    pip install multitfa\n\nTo install from source,\n\n.. code-block:: console\n\n   git clone https://github.com/biosustain/multitfa.git\n   cd multitfa\n   pip install .\n\n\n\nWe highly recommend the installing `CPLEX \u003chttps://www.ibm.com/analytics/cplex-optimizer\u003e`_. Although we support `GUROBI \u003chttps://www.gurobi.com/\u003e`_ solver, we noticed that it is slower and often stuck when solving quadratic constraint problems.\n\nPlease note, Installation takes upto 3 GB. This is to accomodate `equilibrator-api \u003chttps://gitlab.com/equilibrator/equilibrator-api\u003e`_ database files.\n\nInstall Requirements\n====================\n\nInstallation requires\n\n- cobra\n- depinfo\n- optlang\u003c1.4.6\n- numpy\n- scipy\n- pandas\n- equilibrator-api==0.3.2b7\n- component-contribution==0.3.2b4\n- equilibrator-cache==0.3.2b2\n\nfor testing purposes,\n\n- pytest\n- tox\n\nAn example test case was setup to get flux ranges of example script `paper_data_example.py` using `tox`. To run the test case, from inside `multitfa` directory\n\n.. code-block:: console\n\n   pip install tox\n   tox -e examples\n\n\nUsage\n=====\n\nThe documentation is available online at `readthedocs \u003chttps://multitfa.readthedocs.io/en/latest/\u003e`_.\n\nCopyright\n=========\n\n* Copyright © 2018, Novo Nordisk Foundation Center for Biosustainability.\n* Free software distributed under the `Apache Software License 2.0\n  \u003chttps://www.apache.org/licenses/LICENSE-2.0\u003e`_.\n\n\nCite us\n=======\n\nIf you use multitfa in a scientific publication, please cite `doi:10.1101/2020.12.01.407387 \u003chttps://doi.org/10.1101/2020.12.01.407387\u003e`_.\n\nReferences\n==========\n\n.. [1] Henry, Christopher S., Linda J. Broadbelt, and Vassily Hatzimanikatis.\n    \"Thermodynamics-Based Metabolic Flux Analysis.\"\n    *Biophysical Journal* 92, no. 5 (March 1, 2007): 1792–1805.\n    https://doi.org/10.1529/biophysj.106.093138.\n\n.. [2] Vishnuvardhan Mahamkali, Tim McCubbin, Moritz Emanuel Beber, Esteban Marcellin, Lars Keld Nielsen. \n    \"multiTFA: a Python package for multi-variate Thermodynamics-based Flux Analysis.\"\n    *bioRxiv* 2020.12.01.407387;\n    https://doi.org/10.1101/2020.12.01.407387\n\n.. summary-end\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fmultitfa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosustain%2Fmultitfa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fmultitfa/lists"}