{ "info": { "author": "Benjamin Sanchez", "author_email": "bensan@chalmers.se", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6" ], "description": "Please refer to http://geckotoolbox.readthedocs.io\n\n\nHistory\n=======\n\n1.3.5 (2019-05-03)\n------------------\n* Features:\n * Additional options for output tables from ``modifyKcats.m`` & ``topUsedEnzymes.m`` (PR #61)\n * ``keggID`` is now an input for ``updateDatabases.m`` (PR #62)\n * Backwards compatibility with any yeastGEM from 8.0.0 onwards (PR #66)\n * New utilities:\n\t * ``getSubset_ecModel.m``, for getting context-specific ecModels (PR #64)\n * ``getKcat.m``, for retrieving kcats (PR #67)\n* Fixes:\n * Fixed bug in aconitase kcat & misc. error handling (PR #62)\n* Refactoring:\n * Speed improvements in ``topUsedEnzymes.m`` (PR #61)\n * Reduced display of several functions (PR #62)\n * Simplified ``changeMedia_batch.m`` and made more generic ``constrainEnzymes.m`` & ``flexibilizeProteins.m`` (PR #63)\n* Style:\n * Changed EOL to LF (unix default) (PR #68)\n* Documentation:\n * Documented input/output of ``topUsedEnzymes.m`` & ``truncateValues.m`` (PR #61)\n * Added/updated documentation of ``changeMedia_batch.m``, ``constrainEnzymes.m``, ``flexibilizeProteins.m`` & ``getConstrainedModel.m`` (PR #63)\n\n1.3.4 (2018-12-04)\n------------------\n\n* Features:\n * Generalization of ``measureAbundance.m`` to receive any PaxDB file, a relative proteomics dataset, or even nothing at all (PR #58).\n * New utility: Comparative FVA between a model and its enzyme-constrained version (PR #57).\n* Fixes:\n * Consistent definition of what data is in ``uniprot.tab`` (PR #48).\n * Proper use of ``measureAbundance.m`` from within ``constrainEnzymes.m`` (PR #56).\n* Refactoring:\n * Switch all functions that add/change rxns/genes from COBRA to RAVEN (PR #48).\n * Avoid any functions from Simulink (PR #48).\n\n1.3.3 (2018-11-02)\n------------------\n\n* Fixes:\n * Fixes #15: Binary results from the model (``ecModel.mat``, ``ecModel_batch.mat`` & ``enzData.mat``) are no longer stored in repo (PR #52).\n * Misc. fixes in the biomass composition + GAM calculations (PR #53).\n* Refactoring:\n * Speed improvement in misc. functions (PR #49).\n * Added ``sumProtein.m`` for easier use when creating new ecModels (PR #53).\n* Documentation:\n * Documented better which scripts/data should be changed and which are optional when adapting geckomat to produce a new ecModel (PR #53).\n\n1.3.2 (2018-10-12)\n------------------\n* Features:\n * Name & version of the model are now read/stored from/as model fields (PR #42).\n * Pipeline now works for any objective function (PR #47).\n* Fixes:\n * Fixed bug from #39 that saved the ``.mat`` file with the wrong name (PR #42).\n * 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).\n * ``changeMedia_batch.m`` modified to reflect the Y6 minimal media composition (PR #47).\n* Refactoring:\n * Performance improvements to ``getConstrainedModel.m`` and ``sigmaFitter.m`` (PR #47).\n * ``fitGAM.m`` is now only called from inside ``scaleBioMass.m`` (PR #47).\n\n1.3.1 (2018-08-28)\n------------------\n* Features:\n * Adapted the pipeline to work with `yeast-GEM `_, including loading, processing and saving the model. Current model is constructed from yeast `v8.1.3 `_ (PR #39).\n * When constructing ``ecModel_batch``, lipid fraction is now scaled together with protein and carbohydrate fractions (PR #39).\n* Fixes:\n * ``geckopy`` tests flexibilized to comply with yeast-GEM (PR #39).\n* Refactoring:\n * 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).\n * 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).\n * Added `RAVEN `_ as a dependency for ``geckomat`` (PR #38).\n * Changed most COBRA functions in pipeline to RAVEN functions (PR #39).\n\n1.3.0 (2018-08-01)\n------------------\n* Features:\n * 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).\n * Utilities: Included a folder with useful functions (PR #34).\n* Fixes:\n * 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).\n\n1.2.1 (2018-05-30)\n------------------\n* Features:\n * 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.\n * Docs badge in README.\n* Fixes:\n * Fields ``grRules`` and ``rules`` fixed in a consistent way:\n * ``grRules`` for the backwards reactions are the same as for the forward ones.\n * For reactions catalyzed by just 1 enzyme (or complex), ``grRules`` of the original reactions are assigned to them.\n * 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.\n * For enzyme exchange reactions, ``grRules`` are assigned as thecorresponding gene ID.\n * The ``rules`` field is set equal to ``grRules`` for providing consistency with different toolboxes.\n * Inter-OS compatibility:\n * 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.\n * Numbers in all files are shown with up to 6 significant figures.\n* Refactoring:\n * Updated to new COBRA standards for ``addReaction`` usage.\n* NOTE: Not available in pypi (issue #14 unresolved)\n\n1.2.0 (2018-04-12)\n------------------\n* Implemented automatic *kcat* flexibilization for over-constrained models:\n * 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)\n * Once that the model is growing close to the set value, the average enzyme saturation factor is refitted\n * For non-feasible/zero-growth models, sensitivity analysis is performed on a reaction and enzyme basis rather than on individual *kcat* values\n * The outputs of this step are stored in ``topUsedEnzymes.txt`` and ``kcatModification.txt`` and can be used for further manual curation\n* All databases updated (BRENDA, 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