Metadata-Version: 1.1
Name: PyBEL
Version: 0.5.7
Summary: Parsing, validation, and data exchange of BEL graphs
Home-page: https://github.com/pybel/pybel
Author: Charles Tapley Hoyt
Author-email: charles.hoyt@scai.fraunhofer.de
License: Apache 2.0 License
Description: PyBEL |develop_build| |develop_coverage| |develop_documentation| |pypi_license|
        ===============================================================================
        `PyBEL <http://pybel.readthedocs.io>`_ is a Python package for compilation and validation of biological networks
        encoded in the
        `Biological Expression Language <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html>`_ (BEL).
        It also facilitates data interchange between common formats and databases such as
        `NetworkX <http://networkx.github.io/>`_, JSON, CSV, Excel, `Cytoscape <http://www.cytoscape.org/>`_,
        `CX <http://www.home.ndexbio.org/data-model/>`_, `NDEx <https://github.com/pybel/pybel2cx>`_, SQL, and
        `Neo4J <https://neo4j.com>`_. Its companion package, `PyBEL Tools <http://pybel-tools.readthedocs.io/>`_, contains a
        suite of functions and workflows for analyzing the resulting biological networks.
        
        This package was developed at `Fraunhofer SCAI <https://www.scai.fraunhofer.de/>`_
        with support from the `IMI <https://www.imi.europa.eu/>`_ projects: `AETIONOMY <http://www.aetionomy.eu/>`_ and
        `PHAGO <http://www.phago.eu/>`_.
        
        Getting Started
        ---------------
        In this example, the
        `Selventa Small Corpus <https://wiki.openbel.org/display/home/Summary+of+Large+and+Small+BEL+Corpuses>`_ is loaded and
        visualized in a Jupyter Notebook.
        
        .. code-block:: python
        
           >>> import pybel, pybel_tools
           >>> graph = pybel.from_url('http://resources.openbel.org/belframework/20150611/knowledge/small_corpus.bel')
           >>> graph.number_of_nodes()  # Will be smaller than expected because we have the most strict settings enabled
           1207
           >>> pybel_tools.visualization.to_jupyter(graph)
        
        More examples can be found in the `documentation <http://pybel.readthedocs.io>`_ and in the
        `PyBEL Notebooks <https://github.com/pybel/pybel-notebooks>`_ repository.
        
        PyBEL also installs a command line interface with the command :code:`pybel` for simple utilities such as data
        conversion. In this example, a BEL file is exported to GraphML for viewing in Cytoscape.
        
        .. code-block:: sh
        
            $ pybel convert --path ~/Desktop/example.bel --graphml ~/Desktop/example.graphml
           
        In Cytoscape, open with :code:`Import > Network > From File`.
        
        Installation |pypi_version| |python_versions|
        ---------------------------------------------
        PyBEL can be installed easily from `PyPI <https://pypi.python.org/pypi/pybel>`_ with the following code in
        your favorite terminal:
        
        .. code-block:: sh
        
            $ python3 -m pip install pybel
        
        or from the latest code on `GitHub <https://github.com/pybel/pybel>`_ with:
        
        .. code-block:: sh
        
            $ python3 -m pip install git+https://github.com/pybel/pybel.git@develop
        
        See the `installation documentation <http://pybel.readthedocs.io/en/latest/installation.html>`_ for more advanced
        instructions. Also, check the change log at :code:`CHANGELOG.rst`.
        
        Contributing
        ------------
        Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
        :code:`CONTRIBUTING.rst` for more information on getting involved. Please add your name to :code:`AUTHORS.rst`!
        
        Acknowledgements
        ----------------
        - This software is proudly built with Paul McGuire's `PyParsing <http://pyparsing.wikispaces.com/>`_ package.
        - `Scott Colby <https://github.com/scolby33>`_ designed our `logo <https://github.com/pybel/pybel-art>`_ and provided
          sage advice
        - `Christian Ebeling <https://github.com/cebel>`_ for supervision and consultation
        
        Links
        -----
        - Specified by `BEL 1.0 <http://openbel.org/language/web/version_1.0/bel_specification_version_1.0.html>`_ and
          `BEL 2.0 <http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html>`_
        - Documented on `Read the Docs <http://pybel.readthedocs.io/>`_
        - Versioned on `GitHub <https://github.com/pybel/pybel>`_
        - Tested on `Travis CI <https://travis-ci.org/pybel/pybel>`_
        - Distributed by `PyPI <https://pypi.python.org/pypi/pybel>`_
        - Chat on `Gitter <https://gitter.im/pybel/Lobby>`_
        
        
        .. |stable_build| image:: https://travis-ci.org/pybel/pybel.svg?branch=master
            :target: https://travis-ci.org/pybel/pybel
            :alt: Stable Build Status
        
        .. |stable_coverage| image:: https://codecov.io/gh/pybel/pybel/coverage.svg?branch=master
            :target: https://codecov.io/gh/pybel/pybel?branch=master
            :alt: Stable Coverage Status
        
        .. |stable_documentation| image:: https://readthedocs.org/projects/pybel/badge/?version=stable
            :target: http://pybel.readthedocs.io/en/stable/
            :alt: Stable Documentation Status
        
        .. |develop_build| image:: https://travis-ci.org/pybel/pybel.svg?branch=develop
            :target: https://travis-ci.org/pybel/pybel
            :alt: Development Build Status
        
        .. |develop_coverage| image:: https://codecov.io/gh/pybel/pybel/coverage.svg?branch=develop
            :target: https://codecov.io/gh/pybel/pybel?branch=develop
            :alt: Development Coverage Status
        
        .. |develop_documentation| image:: https://readthedocs.org/projects/pybel/badge/?version=latest
            :target: http://pybel.readthedocs.io/en/latest/
            :alt: Development Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/pybel/pybel/badges/gpa.svg
            :target: https://codeclimate.com/github/pybel/pybel
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/PyBEL.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/PyBEL.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/PyBEL.svg
            :alt: Apache 2.0 License
Keywords: Biological Expression Language,BEL,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
