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)
- 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 (2016-2018)
Released under an Apache License.