geckopy 1.3.5

Methods for using the GECKO model with cobrapy

Please refer to http://geckotoolbox.readthedocs.io


History
=======

1.3.5 (2019-05-03)
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* Features:
* Additional options for output tables from ``modifyKcats.m`` & ``topUsedEnzymes.m`` (PR #61)
* ``keggID`` is now an input for ``updateDatabases.m`` (PR #62)
* Backwards compatibility with any yeastGEM from 8.0.0 onwards (PR #66)
* New utilities:
* ``getSubset_ecModel.m``, for getting context-specific ecModels (PR #64)
* ``getKcat.m``, for retrieving kcats (PR #67)
* Fixes:
* Fixed bug in aconitase kcat & misc. error handling (PR #62)
* Refactoring:
* Speed improvements in ``topUsedEnzymes.m`` (PR #61)
* Reduced display of several functions (PR #62)
* Simplified ``changeMedia_batch.m`` and made more generic ``constrainEnzymes.m`` & ``flexibilizeProteins.m`` (PR #63)
* Style:
* Changed EOL to LF (unix default) (PR #68)
* Documentation:
* Documented input/output of ``topUsedEnzymes.m`` & ``truncateValues.m`` (PR #61)
* Added/updated documentation of ``changeMedia_batch.m``, ``constrainEnzymes.m``, ``flexibilizeProteins.m`` & ``getConstrainedModel.m`` (PR #63)

1.3.4 (2018-12-04)
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* Features:
* Generalization of ``measureAbundance.m`` to receive any PaxDB file, a relative proteomics dataset, or even nothing at all (PR #58).
* New utility: Comparative FVA between a model and its enzyme-constrained version (PR #57).
* Fixes:
* Consistent definition of what data is in ``uniprot.tab`` (PR #48).
* Proper use of ``measureAbundance.m`` from within ``constrainEnzymes.m`` (PR #56).
* Refactoring:
* Switch all functions that add/change rxns/genes from COBRA to RAVEN (PR #48).
* Avoid any functions from Simulink (PR #48).

1.3.3 (2018-11-02)
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* Fixes:
* Fixes #15: Binary results from the model (``ecModel.mat``, ``ecModel_batch.mat`` & ``enzData.mat``) are no longer stored in repo (PR #52).
* Misc. fixes in the biomass composition + GAM calculations (PR #53).
* Refactoring:
* Speed improvement in misc. functions (PR #49).
* Added ``sumProtein.m`` for easier use when creating new ecModels (PR #53).
* Documentation:
* Documented better which scripts/data should be changed and which are optional when adapting geckomat to produce a new ecModel (PR #53).

1.3.2 (2018-10-12)
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* Features:
* Name & version of the model are now read/stored from/as model fields (PR #42).
* Pipeline now works for any objective function (PR #47).
* Fixes:
* Fixed bug from #39 that saved the ``.mat`` file with the wrong name (PR #42).
* Adapted pipeline to deal with multiple gene IDs for 1 protein / multiple protein IDs for 1 gene, for dealing with human-based GEMs (PR #43).
* ``changeMedia_batch.m`` modified to reflect the Y6 minimal media composition (PR #47).
* Refactoring:
* Performance improvements to ``getConstrainedModel.m`` and ``sigmaFitter.m`` (PR #47).
* ``fitGAM.m`` is now only called from inside ``scaleBioMass.m`` (PR #47).

1.3.1 (2018-08-28)
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* Features:
* Adapted the pipeline to work with `yeast-GEM <https://github.com/SysBioChalmers/yeast-GEM>`_, including loading, processing and saving the model. Current model is constructed from yeast `v8.1.3 <https://github.com/SysBioChalmers/yeast-GEM/releases/tag/v8.1.3>`_ (PR #39).
* When constructing ``ecModel_batch``, lipid fraction is now scaled together with protein and carbohydrate fractions (PR #39).
* Fixes:
* ``geckopy`` tests flexibilized to comply with yeast-GEM (PR #39).
* Refactoring:
* Reorganized the repo, making a division between ``geckomat`` (Matlab part for generation + simulation of ecModels) and ``geckopy`` (Python part for simulations of ecYeastGEM) (PR #40).
* Parameters ``f`` (mass fraction of enzymes in model), ``Pbase``, ``Cbase``, ``Lbase`` (biomass composition) and ``GAM`` (growth-associated ATP maintenance) are now automatically computed (PR #39).
* Added `RAVEN <https://github.com/SysBioChalmers/RAVEN>`_ as a dependency for ``geckomat`` (PR #38).
* Changed most COBRA functions in pipeline to RAVEN functions (PR #39).

1.3.0 (2018-08-01)
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* Features:
* Protein flexibilization: When proteomic measurements are provided, individual protein levels will now be iteratively flexibilized by the pipeline if the model results to be overconstrained, based on a provided growth rate. After this, flexibilized protein exchange pseudoreaction upper bounds will be set to the their flux values from a parsimonious FBA simulation (PR #34).
* Utilities: Included a folder with useful functions (PR #34).
* Fixes:
* Fixes #14: CI is no longer failing, as model location, model naming and metabolite ID naming were corrected. ``test_adjust_pool_bounds`` was simplified to test with only 1 essential protein (PR #28).

1.2.1 (2018-05-30)
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* Features:
* All genes from the original yeast model now included in the ``.xml`` file. Genes connected to enzyme constraints are now stored in ``model.enzGenes`` in the ``.mat`` structure.
* Docs badge in README.
* Fixes:
* Fields ``grRules`` and ``rules`` fixed in a consistent way:
* ``grRules`` for the backwards reactions are the same as for the forward ones.
* For reactions catalyzed by just 1 enzyme (or complex), ``grRules`` of the original reactions are assigned to them.
* For reactions catalyzed by more than 1 enzyme (or more than 1 complex), ``grRules`` of the original reactions are assigned to the arm reactions, and the corresponding sub-rules are assigned to the isozyme-controlled reactions.
* For enzyme exchange reactions, ``grRules`` are assigned as thecorresponding gene ID.
* The ``rules`` field is set equal to ``grRules`` for providing consistency with different toolboxes.
* Inter-OS compatibility:
* Numbers in scientific notation are stored in the ``.xml`` files with format ``Xe-0N``, not ``Xe-00N``, or with format ``Xe-1N``, not ``Xe-01N``, regardless of the OS used for generating them.
* Numbers in all files are shown with up to 6 significant figures.
* Refactoring:
* Updated to new COBRA standards for ``addReaction`` usage.
* NOTE: Not available in pypi (issue #14 unresolved)

1.2.0 (2018-04-12)
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* Implemented automatic *kcat* flexibilization for over-constrained models:
* Based on a maximum growth rate specified by the user, the algorithm iteratively identifies the top growth-limiting *kcat* value and changes it for the highest one in BRENDA (same EC number)
* Once that the model is growing close to the set value, the average enzyme saturation factor is refitted
* For non-feasible/zero-growth models, sensitivity analysis is performed on a reaction and enzyme basis rather than on individual *kcat* values
* The outputs of this step are stored in ``topUsedEnzymes.txt`` and ``kcatModification.txt`` and can be used for further manual curation
* All databases updated (BRENDA, swissprot, KEGG, PaxDB)
* More generic gene/protein matching for compatibility with other models
* Re-organization of all output files in a single folder
* New badges + styling of website
* NOTE: Not available in pypi (issue #14 unresolved)

1.1.2 (2018-03-20)
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* Improved kcat matching to BRENDA with:
1) Specific activity
2) Phylogenetic distance, when data for organism of choice is not available
* Switched to readthedocs for documentation: http://geckotoolbox.readthedocs.io
* Added a Gitter room for discussion: https://gitter.im/SysBioChalmers/GECKO
* Switched to a simplified GitFlow structure (``master`` + ``devel`` + feature branches)
* Python 3.4 environment dropped in CI (no longer supported by pandas)
* NOTE: Not available in pypi (issue #14 unresolved)

1.1.1 (2017-12-08)
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* Model and data are now also deployed.
* Changes in license and readme.

1.1.0 (2017-09-07)
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* First release on PyPI.

1.0.0 (2017-09-07)
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* First release of GECKO in Github.