https://github.com/cdanielmachado/reframed

ReFramed: metabolic modeling package
https://github.com/cdanielmachado/reframed

metabolism modeling python

Last synced: 5 months ago
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ReFramed: metabolic modeling package

• Host: GitHub
• URL: https://github.com/cdanielmachado/reframed
• Owner: cdanielmachado
• License: other
• Created: 2019-10-01T09:35:10.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2025-09-16T07:34:32.000Z (9 months ago)
• Last Synced: 2025-10-20T00:49:04.676Z (8 months ago)
• Topics: metabolism, modeling, python
• Language: Python
• Homepage:
• Size: 1.07 MB
• Stars: 61
• Watchers: 4
• Forks: 14
• Open Issues: 18
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# 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).

### 💡 New!

A new command-line interface is now available, check the help menu for details:

```

> fba -h

```

### 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)

lMOMA | linear version of 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](https://reframed.readthedocs.io) or try the live demo [here](https://mybinder.org/v2/gh/cdanielmachado/teaching/master?filepath=fba.ipynb).

Latest version was tested with:

- python 3.13

- libsbml 5.20.4

- PySCIPOpt 5.4.1

- Gurobi 12.0.1

- CPLEX 22.1.1 (with python 3.10)

### Credits and License

Developed by Daniel Machado at the Norwegian University of Science and Technology (2025).

**ReFramed** is a refactored version of the [**framed**](https://github.com/cdanielmachado/framed) library.

Released under an Apache License.