reframed 1.6.0

metabolic modeling package

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)

Credits and License

Developed by Daniel Machado at the Norwegian University of Science and Technology (NTNU).

ReFramed is a refactored version of the framed library.

Released under an Apache License.