Metadata-Version: 1.1
Name: geckopy
Version: 1.3.0
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: ../README.rst
        
        
        History
        =======
        
        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
