Description:
framed 0.5.2
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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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