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DOI License PyPI version Documentation Status

Note: this package will soon be deprecated! Please check the new ReFramed package.

FRAMED

A python FRAmework for Metabolic Engineering and Design

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 multiple SBML flavors and plain text formats (including BioOpt)
  • Solver support: Gurobi, CPLEX
  • COBRA tools:
    • Simulation: FBA, pFBA, loopless-FBA, MOMA, linearMOMA, ROOM
    • Gene-wise simulation: gene-pFBA, gene-MOMA, gene-lMOMA, gene-ROOM
    • Analysis: FVA, gene essentiality, PhPP, flux envelope plots
    • Ensemble-based simulation (includes import/export of ensemble models in SBML)
    • Omics integration: GIMME, E-Flux
  • Kinetic tools:
    • Time-course and steady-state simulation
    • Steady-state flux sampling
    • Calibration from metabolomics data
  • Bioprocess modeling:
    • Dynamic FBA (single and multi-species)

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 (2016-2018)

Released under an Apache License.