Metadata-Version: 2.1
Name: PyBEL
Version: 0.12.1
Summary: Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)
Home-page: https://github.com/pybel/pybel
Author: Charles Tapley Hoyt
Author-email: charles.hoyt@scai.fraunhofer.de
Maintainer: Charles Tapley Hoyt
Maintainer-email: charles.hoyt@scai.fraunhofer.de
License: Apache 2.0 License
Description: PyBEL |zenodo|
        ==============
        `PyBEL <http://pybel.readthedocs.io>`_ is a pure Python package for parsing and handling 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, SIF, `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 pipelines for analyzing the resulting biological networks.
        
        We realize there we have a name conflict with the python wrapper for the cheminformatics package, OpenBabel. If you're
        looking for their python wrapper, see `here <https://github.com/openbabel/openbabel/tree/master/scripts/python>`_.
        
        =========== =============== ======================= ================== =======================
        Stable      |stable_build|  |stable_windows_build|  |stable_coverage|  |stable_documentation|
        Development |develop_build| |develop_windows_build| |develop_coverage| |develop_documentation|
        =========== =============== ======================= ================== =======================
        
        Citation
        --------
        If you use PyBEL in your work, please cite:
        
        .. [1] Hoyt, C. T., *et al.* (2017). `PyBEL: a Computational Framework for Biological Expression Language <https://doi.org/10.1093/bioinformatics/btx660>`_. Bioinformatics, 34(December), 1–2.
        
        Getting Started
        ---------------
        This example illustrates how the `Selventa Small Corpus <https://wiki.openbel.org/display/home/Summary+of+Large+and+Small+BEL+Corpuses>`_
        can be loaded and visualized in a Jupyter Notebook. Note that this requires an extension, the ``pybel-jupyter``
        repository. This is not included by default because installing the Jupyter and iPython stack has a large footprint.
        
        .. code-block:: python
        
           >>> import pybel, pybel_jupyter
           >>> 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_jupyter.to_jupyter(graph)  # Need to pip install pybel-jupyter first
        
        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 Script 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| |pypi_license|
        ------------------------------------------------------------
        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 package was originally developed as part of the master's work of
          `Charles Tapley Hoyt <https://github.com/cthoyt>`_ at `Fraunhofer SCAI <https://www.scai.fraunhofer.de/>`_.
        - 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/version_1.0/bel_specification_version_1.0.html>`_ and
          `BEL 2.0 <http://openbel.org/language/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_windows_build| image:: https://ci.appveyor.com/api/projects/status/v22l3ymg3bdq525d/branch/master?svg=true
            :target: https://ci.appveyor.com/project/cthoyt/pybel
            :alt: Stable Windows 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_windows_build| image:: https://ci.appveyor.com/api/projects/status/v22l3ymg3bdq525d/branch/develop?svg=true
            :target: https://ci.appveyor.com/project/cthoyt/pybel
            :alt: Development Windows 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
        
        .. |zenodo| image:: https://zenodo.org/badge/68376693.svg
            :target: https://zenodo.org/badge/latestdoi/68376693
        
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
Provides-Extra: indra
Provides-Extra: neo4j
