framed: a metabolic modeling package for python
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
doc
examples
framed.egg-info
scripts
src/framed
.gitignore
LICENSE
README.md
README.rst
logo_300px.png
setup.cfg
setup.py

README.md

DOI License PyPI version Documentation Status

FRAMED

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.