framed 0.5.2

framed - metabolic modeling for python

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.