framed - metabolic modeling for python
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
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
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: http://framed.readthedocs.io/
pip install framed
Credits and License
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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