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ReFramed: metabolic modeling package

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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, cobrapy, and optlang.

Available methods

Name Long name Reference
FBA Flux Balance Analysis (Varma and Palsson, 1993)
FVA Flux Variability Analysis (Mahadevan and Schilling, 2003)
pFBA Parsimonious FBA (Lewis et al, 2010)
FBrAtio FBA with flux ratios (Yen et al, 2013)
CAFBA Constrained Allocation FBA (Mori et al, 2016)
MOMA Minimization of Metabolic Adjustment (Segre et al, 2002)
lMOMA linear MOMA (Segre et al, 2002)
ROOM Regulatory On/Off Minimization (Shlomi et al, 2005)
ll-FBA loopless FBA (Schellenberger et al, 2011)
TFA Thermodynamic Flux Analysis (Henry et al, 2007)
TVA Thermodynamic Variability Analysis (Henry et al, 2007)
NET Network-embedded thermodynamic analysis (Kummel et al 2006)
GIMME Gene Inactivity Moderated by Met and Exp (Becker and Palsson, 2008)
E-Flux E-Flux (Colijn et al, 2009)
SteadyCom Community simulation (Chan et al, 2017)

Documentation

Please check documentation with installation and usage instructions here or try the live demo here.

Credits and License

Developed by Daniel Machado at the European Molecular Biology Laboratory (2019).

ReFramed is a refactored version of the framed library.

Released under an Apache License.