Metadata-Version: 1.2
Name: reframed
Version: 1.2.1
Summary: metabolic modeling package
Home-page: https://github.com/cdanielmachado/reframed
Author: Daniel Machado
Author-email: cdanielmachado@gmail.com
License: Apache Software License 2.0
Description: .. 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 European Molecular Biology Laboratory
        (2019).
        
        **ReFramed** is a refactored version of the
        `framed <https://github.com/cdanielmachado/framed>`__ library.
        
        Released under an Apache License.
        
Keywords: reframed
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
