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Version 1.2

Crucial edit to setup.py file

Adding PyFBA.model package to list.

Version 1.1

Updated all the code to work with Python 3.

However, this breaks compatibility with Python 2 because of the "errors" keyword in open.

The main changes include relative imports, a new class in the tests/ package to allow deep assertions, and using this type of construct with the open command to ignore unicode errors in ModelSeed:

with open(ssfile, 'r', errors='replace') as sin:

Added function to obtain Model SEED complexes from a set of roles

  • PyFBA/filters/roles_and_complexes.py

Added gap-fill step to add reactions based on existent EC numbers

  • PyFBA/gapfill/ecnumbers.py

Optimized and fixed bugs during gap-fill reaction minimization process

  • PyFBA/gapfill/reaction_minimization.py

New Model class objects

Model object contains functionality to make common processes easier to facilitate.

  • Generate model from RAST annotations
  • Save model to hard disk location
  • Load model from hard disk location
  • Run FBA
  • Run FBA and obtain flux values
  • Run FBA and obtain flux values according to SEED subsystems
  • Run gap-fill
  • Remember which reactions were gap-filled reactions and which media

New iPython Notebooks

  • Find a metabolite.ipynb
  • PATRIC to FBA.ipynb
  • Gap-fill_a_model.ipynb
  • Saving_and_loading_a_model.ipynb

Version 1.0

Added a CITATION.md

Please cite us if you use PyFBA

Added the iPython Notebook directory

Example code showing:

importing an SBML file and running FBA

  • iPythonNotebooks/Using_an_SBML_model.ipynb

how to build your model from functional roles and how to gap-fill that model on a media

  • iPythonNotebook/From_functional_roles_to_gap-filling.ipynb

Added minimization by accuracy

Removed PyFBA/gapfill/minimize_additional_reactions.py and created reaction_minimization.py

Example gap-fill pipeline

  • example_code/gapfill_from_reactions_multiple_conditions.py

Version 0.951

Removed the author tag

It is superflous, that is what versioning is for.

Version 0.95

Several changes to files:

Updated the subsystem functions and changed the name to a generic name. The date is handled by versioning!

  • PyFBA/Biochemistry/SEED/Subsystems/SS_functions.txt
  • PyFBA/Biochemistry/SEED/Subsystems/SS_functions_Oct_2015.txt

Changing the version number

  • PyFBA/init.py

Adding reaction flux information that can be pulled after the sm has been solved

  • PyFBA/fba/init.py
  • PyFBA/fba/fluxes.py

External reactions

Fixed an issue where we were over-incorporating reactions based on things in the media

  • PyFBA/fba/bounds.py
  • PyFBA/parse/model_seed.py

Adding verboseness

  • PyFBA/fba/run_fba.py
  • PyFBA/gapfill/roles.py
  • PyFBA/parse/read_media.py

Reduced complexity

We only test the right half of the reactions if the left half do not grow, and once we have <10 reactions to search through we just iterate and knock out each reaction sequentially. It is faster than the shuffle approach.

  • PyFBA/gapfill/minimize_additional_reactions.py

Changed the way we read roles

SEED has a notion of multifunctional roles, and we added splitting those functions into roles

  • PyFBA/gapfill/subsystem.py

Gap generation code

Testing each of the individual reactions in a model

  • PyFBA/gapgeneration/test_reactions.py
  • example_code/test_individual_reactions.py

Shifted the order of gapfilling

This order makes more logical sense!

  • example_code/gapfill_from_reactions.py

Updated the tests

With all these changes, the tests were not right

  • PyFBA/tests/reaction_list.txt
  • PyFBA/tests/test_fba.py
  • PyFBA/tests/test_suggestions.py

Version 0.9

Refactored separating roles to functions. SEED has a concept of multifunctional roles and this separates out our roles before we search for them.

Version 0.8

Version 0.7

Version 0.6

  • Removed installation dependencies from setup.py because they break installation! You need to install the dependencies manually
  • Refactored the code to remove the os.environ dependencies

Version 0.5

  • Initial release