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