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        "description": ".. figure:: reframed_logo.png\n   :alt: ReFramed\n\n   ReFramed\n\nReFramed: metabolic modeling package\n====================================\n\n**ReFramed** implements many constraint-based simulation methods (see\nlist below), and contains interfaces to other libraries of the *COBRA*\necosystem including `escher <https://escher.github.io>`__,\n`cobrapy <https://opencobra.github.io/cobrapy/>`__, and\n`optlang <https://github.com/biosustain/optlang>`__.\n\nAvailable methods\n-----------------\n\n+-----------------------+-----------------------+-----------------------+\n| Name                  | Long name             | Reference             |\n+=======================+=======================+=======================+\n| FBA                   | Flux Balance Analysis | (Varma and Palsson,   |\n|                       |                       | 1993)                 |\n+-----------------------+-----------------------+-----------------------+\n| FVA                   | Flux Variability      | (Mahadevan and        |\n|                       | Analysis              | Schilling, 2003)      |\n+-----------------------+-----------------------+-----------------------+\n| pFBA                  | Parsimonious FBA      | (Lewis et al, 2010)   |\n+-----------------------+-----------------------+-----------------------+\n| FBrAtio               | FBA with flux ratios  | (Yen et al, 2013)     |\n+-----------------------+-----------------------+-----------------------+\n| CAFBA                 | Constrained           | (Mori et al, 2016)    |\n|                       | Allocation FBA        |                       |\n+-----------------------+-----------------------+-----------------------+\n| MOMA                  | Minimization of       | (Segre et al, 2002)   |\n|                       | Metabolic Adjustment  |                       |\n+-----------------------+-----------------------+-----------------------+\n| lMOMA                 | linear MOMA           | (Segre et al, 2002)   |\n+-----------------------+-----------------------+-----------------------+\n| ROOM                  | Regulatory On/Off     | (Shlomi et al, 2005)  |\n|                       | Minimization          |                       |\n+-----------------------+-----------------------+-----------------------+\n| ll-FBA                | loopless FBA          | (Schellenberger et    |\n|                       |                       | al, 2011)             |\n+-----------------------+-----------------------+-----------------------+\n| TFA                   | Thermodynamic Flux    | (Henry et al, 2007)   |\n|                       | Analysis              |                       |\n+-----------------------+-----------------------+-----------------------+\n| TVA                   | Thermodynamic         | (Henry et al, 2007)   |\n|                       | Variability Analysis  |                       |\n+-----------------------+-----------------------+-----------------------+\n| NET                   | Network-embedded      | (Kummel et al 2006)   |\n|                       | thermodynamic         |                       |\n|                       | analysis              |                       |\n+-----------------------+-----------------------+-----------------------+\n| GIMME                 | Gene Inactivity       | (Becker and Palsson,  |\n|                       | Moderated by Met and  | 2008)                 |\n|                       | Exp                   |                       |\n+-----------------------+-----------------------+-----------------------+\n| E-Flux                | E-Flux                | (Colijn et al, 2009)  |\n+-----------------------+-----------------------+-----------------------+\n| SteadyCom             | Community simulation  | (Chan et al, 2017)    |\n+-----------------------+-----------------------+-----------------------+\n\nCredits and License\n-------------------\n\nDeveloped by Daniel Machado at the European Molecular Biology Laboratory\n(2019).\n\n**ReFramed** is a refactored version of the\n`framed <https://github.com/cdanielmachado/framed>`__ library.\n\nReleased under an Apache License.\n\n\n",
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