Metadata-Version: 1.1
Name: PyFBA
Version: 1.1
Summary: A Python implementation of flux balance analysis
Home-page: http://linsalrob.github.io/PyFBA/
Author: Rob Edwards
Author-email: raedwards@gmail.com
License: The MIT License (MIT)
Description: PyFBA
        =====
        
        A python implementation of flux balance analysis to model microbial
        metabolism
        
        About PyFBA
        -----------
        
        PyFBA is a Python flux-balance-analysis package that allows you to build
        models from genomes, gapfill models, and run flux-balance-analysis on
        that model. The aim of PyFBA is to provide an extensible, python-based
        platform for FBA work.
        
        PyFBA is being developed by Daniel Cuevas, Taylor O'Connell, and Rob
        Edwards in Rob's bioinformatics group at San Diego State University
        together with help from Janaka Edirisinghe, Chris Henry, Ross Overbeek
        and others at Argonne National Labs.
        
        Installing PyFBA
        ----------------
        
        To use PyFBA you need Python 2.7 or greater, and you need to install the
        GNU GLPK and a Python wrapper for that program, pyGLPK available from
        github.
        
        We also leverage the Model SEED GitHub repository with all the latest
        biochemistry tables.
        
        Our installation page has detailed instructions on installing PyFBA and
        getting everything running.
        
        Getting Started with PyFBA
        --------------------------
        
        Once you have installed GLPK, PyGLPK, and PyFBA, you will most likely
        want to build a model from a genome, gap fill that model, and test it
        for growth on different media. We have detailed instructions that walk
        you through the step-by-step procedures that you need to use to run flux
        balance analysis on your own genome.
        
        Copyright and License
        
        PyFBA is copyright Daniel Cuevas, Taylor O'Connell, and Rob Edwards, and
        is released under the MIT license.
        
        
        
        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
        
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.0
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
