Metadata-Version: 1.1
Name: geckopy
Version: 2.0.1
Summary: Methods for using the GECKO model with cobrapy
Home-page: https://github.com/SysBioChalmers/GECKO/tree/master/geckopy
Author: Benjamin Sanchez
Author-email: bensan@chalmers.se
License: MIT License
Description: Please refer to http://geckotoolbox.readthedocs.io
        
        
        History
        =======
        
        2.0.1 (2020-11-19)
        ------------------
        * Fixes:
            * UBs are only changed for strictly required proteins (PR #103).
            * Solves #101: All yeast models in the toolbox are built on the same yeast-GEM version `8.1.3 <https://github.com/SysBioChalmers/yeast-GEM/releases/tag/v8.1.3>`_ (PR #105).
            * Solved bug in ``generate_protModels.m`` that constrained both the biomass and growth reactions (PR #107).
            * Updated env. list after release of pandas 1.0 (PR #110).
            * A folder for ecModels is added in case it doesn’t exist already (PR #111).
            * Solves #112: Avoid using the variable name ``version`` for potential conflicts with Matlab (PR #113).
        * Style:
            * Solves #102: All UBs in repo changed from +Inf to +1000 (PR #109).
        
        2.0.0 (2020-05-18)
        ------------------
        * Features:
            * A main utility for constraining an ecModel with proteomics data stored in data files, and ensuring the model can grow at the provided conditions (PR #82).
            * More constraining options in FVA utility (PR #95).
            * An option for reducing display of ``fitGAM.m`` (PR #82).
            * A chemostat simulation utility (PR #82).
        * Fixes:
            * Fixes #73: Bug in ``getKcat.m`` (PR #75).
            * Fixes #78: Updated BRENDA URL (PR #91).
            * FVA utility: Fixed directionality bugs in ``MAX_min_Optimizer.m`` (PRs #69 & #95) & optimization bug in ``comparativeFVA.m`` (PR #95).
            * geckopy: Updated csv reader in geckopy test (PR #83) and met id parsing (PR #93).
            * Fixed subfolder bug in ``modifyKcats.m`` (PR #80).
        * Refactoring:
            * Introduced ``getModelParameters.m`` for defining all input parameters, for streamlining the main ecModel generation pipeline (PR #76).
            * Simplified constraining procedure in the FVA utility (PR #95).
        * Documentation:
            * Improved documentation of several main functions (PR #76).
            * Updated Matlab requirements (PR #96).
        
        1.3.5 (2019-05-03)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * 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)
        ------------------
        * Model and data are now also deployed.
        * Changes in license and readme.
        
        1.1.0 (2017-09-07)
        ------------------
        * First release on PyPI.
        
        1.0.0 (2017-09-07)
        ------------------
        * First release of GECKO in Github.
        
Keywords: geckopy
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
