Metadata-Version: 1.1
Name: PyBEL
Version: 0.3.11
Summary: Parsing, validation, and analysis 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
        =====
        
        :code:`PyBEL` is a Python software package that parses BEL scripts, validates their semantics, applies common graph
        algorithms, and facilitates data interchange between common formats and database systems like JSON, CSV, SQL, and Neo4J.
        
        =========== =============== ================== =======================
        Stable      |stable_build|  |stable_coverage|  |stable_documentation| 
        Development |develop_build| |develop_coverage| |develop_documentation|
        =========== =============== ================== =======================
        
        
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            :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
        
        
        Biological Expression Language (BEL) is a domain-specific language that enables the expression of complex molecular
        relationships and their context in a machine-readable form. Its simple grammar and expressive power have led to its
        successful use in the `IMI <https://www.imi.europa.eu/>`_ project, `AETIONOMY <http://www.aetionomy.eu/>`_, to describe
        complex disease networks with several thousands of relationships.
        
        :code:`PyBEL` provides a simple API so bioinformaticians and scientists with limited programming knowledge can easily
        use it to interface with BEL graphs, but is built on a rich framework that can be extended to develop new algorithms.
        
        .. code-block:: python
        
           >>> import pybel, networkx
           >>> g = pybel.from_url('http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel')
           >>> networkx.draw(g)  # NOTE: requires matplotlib as a dependency, which isn't automatically installed
        
        PyBEL also installs a command line interface with the command :code:`pybel` for simple utilities such as data
        conversion. Need help? All logs go to :code:`~/.pybel` or add :code:`-v` for verbose output to the standard error
        stream. 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| |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
        
           pip install pybel
        
        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.
        
        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
        - Core Team: `Charles Tapley Hoyt <https://github.com/cthoyt>`_, `Andrej Konotopez <https://github.com/lekono>`_, and `Christian Ebeling <https://github.com/cebel>`_
        
        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>`_
        
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 :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
