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framed - metabolic modeling for python

Project description


framed is a python package for analysis and simulation of metabolic models. The main focus is to provide support for different modeling approaches.

  • Modeling: Constraint-based models, Kinetic models, Bioprocess models

  • I/O: Import/Export from SBML and/or plain text formats

  • Solver support: Gurobi, CPLEX, GLPK

  • COBRA tools:

    • Simulation: FBA, pFBA, loopless-FBA, MOMA, linearMOMA, ROOM

    • Analysis: FVA, gene essentiality, PhPP, flux envelope plots

    • Omics integration: GIMME, E-Flux

    • Strain design: brute force, hill climbing

  • Kinetic tools:

    • Time-course and steady-state simulation

    • Parameter and flux sampling

    • Calibration from metabolomics data

  • Bioprocess modeling: Dynamic FBA (single and multi-species)


For documentation and API please check:


pip install framed

Credits and License

Developed at:

  • The Novo Nordisk Fundation Center for Biosustainability (2013)

  • Centre of Biological Engineering, University of Minho (2014-2015)

  • European Molecular Biology Laboratory (2016)

Released under an Apache License.

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