Metadata-Version: 2.1
Name: pybel
Version: 0.14.6
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: cthoyt@gmail.com
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Download-URL: https://github.com/pybel/pybel/releases
Project-URL: Bug Tracker, https://github.com/pybel/pybel/issues
Project-URL: Source Code, https://github.com/pybel/pybel
Project-URL: Documentation, https://pybel.readthedocs.io
Description: PyBEL |zenodo| |build| |windows_build| |coverage| |documentation|
        =================================================================
        `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, JGIF, 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 that 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>`_.
        
        Citation
        --------
        If you find PyBEL useful for your work, please consider citing:
        
        .. [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.
        
        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 shell:
        
        .. code-block:: sh
        
            $ pip install pybel
        
        or from the latest code on `GitHub <https://github.com/pybel/pybel>`_ with:
        
        .. code-block:: sh
        
            $ pip install git+https://github.com/pybel/pybel.git
        
        See the `installation documentation <https://pybel.readthedocs.io/en/latest/introduction/installation.html>`_ for more advanced
        instructions. Also, check the change log at `CHANGELOG.rst <https://github.com/pybel/pybel/blob/master/CHANGELOG.rst>`_.
        
        Note: while PyBEL works on the most recent versions of Python 3.5, it does not work on 3.5.3 or below due to changes
        in the ``typing`` module.
        
        Getting Started
        ---------------
        More examples can be found in the `documentation <http://pybel.readthedocs.io>`_ and in the
        `PyBEL Notebooks <https://github.com/pybel/pybel-notebooks>`_ repository.
        
        Compiling a BEL Graph
        ~~~~~~~~~~~~~~~~~~~~~
        This example illustrates how the a BEL document from the `Human Brain Pharmacome
        <https://raw.githubusercontent.com/pharmacome/knowledge>`_ project can be loaded from GitHub.
        
        .. code-block:: python
        
           >>> import pybel
           >>> url = 'https://raw.githubusercontent.com/pharmacome/knowledge/master/hbp_knowledge/proteostasis/kim2013.bel'
           >>> graph = pybel.from_url(url)
        
        PyBEL can handle `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>`_ simultaneously.
        
        Displaying a BEL Graph in Jupyter
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        After installing ``jinja2`` and ``ipython``, BEL graphs can be displayed in Jupyter notebooks.
        
        .. code-block:: python
        
           >>> from pybel.examples import sialic_acid_graph
           >>> from pybel.io.jupyter import to_jupyter
           >>> to_jupyter(sialic_acid_graph)
        
        Using the CLI
        ~~~~~~~~~~~~~
        PyBEL also installs a command line interface with the command :code:`pybel` for simple utilities such as data
        conversion. In this example, a BEL document is compiled then exported to `GraphML <http://graphml.graphdrawing.org/>`_
        for viewing in Cytoscape.
        
        .. code-block:: sh
        
            $ pybel compile ~/Desktop/example.bel
            $ pybel serialize ~/Desktop/example.bel --graphml ~/Desktop/example.graphml
        
        In Cytoscape, open with :code:`Import > Network > From File`.
        
        Contributing
        ------------
        Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
        `CONTRIBUTING.rst <https://github.com/pybel/pybel/blob/master/CONTRIBUTING.rst>`_ for more information on getting
        involved.
        
        Acknowledgements
        ----------------
        Supporters
        ~~~~~~~~~~
        This project has been supported by several organizations:
        
        - `University of Bonn <https://www.uni-bonn.de>`_
        - `Bonn Aachen International Center for IT <http://www.b-it-center.de>`_
        - `Fraunhofer Institute for Algorithms and Scientific Computing <https://www.scai.fraunhofer.de>`_
        - `Fraunhofer Center for Machine Learning <https://www.cit.fraunhofer.de/de/zentren/maschinelles-lernen.html>`_
        - `The Cytoscape Consortium <https://cytoscape.org/>`_
        
        Logo
        ~~~~
        The PyBEL `logo <https://github.com/pybel/pybel-art>`_ was designed by `Scott Colby <https://github.com/scolby33>`_.
        
        .. |build| image:: https://travis-ci.org/pybel/pybel.svg?branch=develop
            :target: https://travis-ci.org/pybel/pybel
            :alt: Development Build Status
        
        .. |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
        
        .. |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
        
        .. |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
            :target: https://pypi.python.org/pypi/pybel
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/PyBEL.svg
            :target: https://pypi.python.org/pypi/pybel
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/PyBEL.svg
            :target: https://github.com/pybel/pybel/blob/master/LICENSE
            :alt: MIT License
        
        .. |zenodo| image:: https://zenodo.org/badge/68376693.svg
            :target: https://zenodo.org/badge/latestdoi/68376693
        
Keywords: Biological Expression Language,BEL,Domain Specific Language,DSL,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.5
Provides-Extra: indra
Provides-Extra: jupyter
Provides-Extra: neo4j
Provides-Extra: docs
