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framed - metabolic modeling for python

Project description

DOI License PyPI version Documentation Status

FRAMED

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 other 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 (and SBML import/export of ensemble models)

    • Omics integration: GIMME, E-Flux

    • Strain design: brute force, hill climbing

  • Kinetic tools:

    • Time-course and steady-state simulation

    • Steady-state flux sampling

    • Calibration from metabolomics data

  • Bioprocess modeling:

    • Dynamic FBA (single and multi-species)

  • Microbial community modeling:

    • SMETANA

Documentation

For documentation and API please check: http://framed.readthedocs.io/

Instalation from PyPI (stable releases)

pip install framed

Instalation from github (latest development release)

pip install https://github.com/cdanielmachado/framed/archive/master.zip

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 (2016-2017)

Released under an Apache License.

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