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Status](https://travis-ci.org/cdanielmachado/reframed.svg?branch=master)](https://travis-ci.org/cdanielmachado/reframed)\n[![Documentation Status](https://readthedocs.org/projects/reframed/badge/?version=latest)](https://reframed.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://zenodo.org/badge/212059108.svg)](https://zenodo.org/badge/latestdoi/212059108)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cdanielmachado/teaching/master?filepath=fba.ipynb)\n\n![ReFramed](reframed_logo.png)\n\n# ReFramed: metabolic modeling package\n\n**ReFramed** implements many constraint-based simulation methods (see list below), and contains interfaces to other\nlibraries of the *COBRA* ecosystem including [**escher**](https://escher.github.io),\n[**cobrapy**](https://opencobra.github.io/cobrapy/), and [**optlang**](https://github.com/biosustain/optlang).\n\n### 💡 New!\n\nA new command-line interface is now available, check the help menu for details:\n\n```\n\u003e fba -h\n```\n\n### Available methods\n\nName | Long name | Reference\n--- | --- | ---\nFBA | Flux Balance Analysis | (Varma and Palsson, 1993)\nFVA | Flux Variability Analysis | (Mahadevan and Schilling, 2003)\npFBA | Parsimonious FBA | (Lewis et al, 2010)\nFBrAtio | FBA with flux ratios| (Yen et al, 2013)\nCAFBA | Constrained Allocation FBA | (Mori et al, 2016)\nlMOMA | linear version of MOMA | (Segre et al, 2002)\nROOM | Regulatory On/Off Minimization | (Shlomi et al, 2005)\nll-FBA | loopless FBA | (Schellenberger et al, 2011)\nTFA | Thermodynamic Flux Analysis | (Henry et al, 2007)\nTVA | Thermodynamic Variability Analysis | (Henry et al, 2007)\nNET | Network-embedded thermodynamic analysis |  (Kummel et al 2006)\nGIMME | Gene Inactivity Moderated by Met and Exp | (Becker and Palsson, 2008)\nE-Flux | E-Flux | (Colijn et al, 2009)\nSteadyCom | Community simulation | (Chan et al, 2017)\n\n### Documentation\n\nPlease check documentation with installation and usage instructions [here](https://reframed.readthedocs.io) or try the live demo [here](https://mybinder.org/v2/gh/cdanielmachado/teaching/master?filepath=fba.ipynb).\n\nLatest version was tested with:\n\n- python 3.13\n- libsbml 5.20.4\n- PySCIPOpt 5.4.1\n- Gurobi 12.0.1\n- CPLEX 22.1.1 (with python 3.10)\n\n### Credits and License\n\nDeveloped by Daniel Machado at the Norwegian University of Science and Technology (2025).\n\n**ReFramed** is a refactored version of the [**framed**](https://github.com/cdanielmachado/framed) library.\n\nReleased under an Apache License.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdanielmachado%2Freframed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcdanielmachado%2Freframed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdanielmachado%2Freframed/lists"}