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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.

Github

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Dependencies

Used By

Total: 0

Releases

0.5.0 - May 28, 2018

This release introduces Python 3 compatibility. For the moment both Python 2 and Python 3 will be supported (we may drop support for Python 2 at some point in the future).

Other updates include bug fixes and speed improvements in gurobi and cplex interfaces.

SMETANA was removed from framed and will have its own dedicated repository.

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!)