Bug fix release

0.5.2

bump to 0.5.2

First python 3 compatible release

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.

Even more features

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

new features

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

Bug fix release

• 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

Major overall changes

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!)

Now with pip installer

First release prepared for pip installation.

First stable release after major refactoring

Includes several changes with regard to the last release, including:

• Refactoring of the model classes (now called: Model, CBModel, and ODEModel)
• Support for sbml-fbc2
• New CPLEX wrapper
• Implemented looplessFBA
• New DataSet class to load multi-omics datasets from JSON files
• Implemented two omics-based methods (GIMME, E-Flux)
• New module with kinetic modeling utilities (simulation, steady-state analysis, calibration, sampling)
• Kinetic models now support assignment rules

Last stable beta before major refactoring

Last stable beta before major refactoring