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cdanielmachado
ReFramed: metabolic modeling package
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.
cdanielmachado