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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.

Github

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Dependencies

Used By

Total: 0

Releases

0.4.0 - Nov 13, 2017

This version introduces several new features including:

  • Ensemble modeling with cobra models (including SBML import/export and FBA/pFBA simulation, similar to the EnsembleFBA methodology proposed by Biggs and Papin: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005413)
  • Gene-wise simulation methods (gene-pFBA, gene-MOMA, gene-lMOMA, gene-ROOM, as defined in: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005140)
  • Base classes giving support for microbial community modeling
  • SMETANA tools for analysing microbial communities (as defined in: http://www.pnas.org/content/112/20/6449.short)
  • New BioOpt format parser
  • Extended SBML flavors (cobra, fbc2, seed, bigg, other)
  • New Environment class to define the extracellular environments from medium compositions and direct integration with CBModel class
  • Improved parsing of kinetic models

Also:

  • Discontinued support for GLPK
  • Multiple bug fixes

0.3.2 - Jan 12, 2017

  • MetaNetX translation service
  • Thermodynamics-based methods (TMFA and NET)
  • Visualisation: KEGG and Escher support (experimental)
  • New Medium class
  • Improvements to solver interface

0.3.1 - Nov 10, 2016

  • don’t import everything to top-level
  • speedup metabolite deletion
  • implement copy in AttrOrderedDict
  • clean compartments in simplify method
  • print reduced costs in solution class
  • improve gpr and metadata parser
  • don't rebuild ODEs in kinetic model

0.3.0 - Oct 26, 2016

This release includes several significant changes:

  • refactoring of the module hierarchy
  • imports now directly from top-level package
  • improved docstrings
  • new CBReaction class with cobra-specific attributes
  • model.reactions and model.metabolites now support indexing by attribute name (similar to cobrapy)
  • simplification of solver classes
  • created documentation hosted at ReadTheDocs (finally!)

v0.2.1 - Sep 28, 2016

First release prepared for pip installation.