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