README.rst

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.