Metadata-Version: 2.1
Name: bel_commons
Version: 0.3.0
Summary: A web application exposing core PyBEL functionalities
Home-page: https://github.com/bel-commons/bel-commons
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/bel-commons/bel-commons/releases
Project-URL: Bug Tracker, https://github.com/bel-commons/bel-commons/issues
Project-URL: Source Code, https://github.com/bel-commons/bel-commons
Description: BEL Commons |build| |docs|
        ==========================
        An environment for curating, validating, and exploring knowledge assemblies
        encoded in Biological Expression Language (BEL) to support elucidating
        disease-specific, mechanistic insight.
        
        Installation
        ~~~~~~~~~~~~
        BEL Commons can be installed easily from `PyPI <https://pypi.python.org/pypi/bel_commons>`_ with the following code in
        your favorite shell:
        
        .. code-block:: sh
        
            $ pip install bel_commons
        
        Get the latest code on `GitHub <https://github.com/bel-commons/bel-commons>`_
        with:
        
        .. code-block:: sh
        
            $ python3 -m pip install git+https://github.com/bel-commons/bel-commons.git
        
        It's also suggested to use a relational database management system like PostgreSQL
        and install their corresponding connectors:
        
        .. code-block:: sh
        
            $ python3 -m pip install psycopg2-binary
        
        Usage
        -----
        Run BEL Commons
        ~~~~~~~~~~~~~~~
        A test server can be easily run with:
        
        .. code-block:: sh
        
            $ bel-commons run
        
        A more powerful server like ``gunicorn`` can also be used like:
        
        .. code-block:: sh
        
            $ gunicorn bel_commons.wsgi:flask_app
        
        Running with the Parser
        ~~~~~~~~~~~~~~~~~~~~~~~
        To run the parser, you'll need an instance of a message queue like `RabbitMQ <https://www.rabbitmq.com>`_ (or
        any other message queue supported by `Celery <https://pypi.python.org/pypi/celery>`_), a results backend like
        `Redis <https://redis.io/>`_, and a worker. It's best to run in docker if you want to do this.
        
        Run with Docker
        ~~~~~~~~~~~~~~~
        Clone this repo from GitHub
        
        .. code-block:: sh
        
           $ git clone https://github.com/bel-commons/bel-commons.git
           $ cd bel-commons
        
        Create a file called ``.env`` and generate both ``SECRET_KEY`` and ``SECURITY_PASSWORD_SALT``.
        
        .. code-block:: sh
        
            SECRET_KEY=mypassword
            SECURITY_PASSWORD_SALT=mypassword
        
        Run docker compose:
        
        .. code-block:: sh
        
            $ docker-compose up
        
        Ports exposed:
        
        - 5002: BEL Commons web application
        - 5432: PostgreSQL database
        
        
        Reset the Database
        ~~~~~~~~~~~~~~~~~~
        For the times when you just have to burn it down and start over:
        
        1. ``bel-commons manage drop`` will nuke the database and output a user list
        2. ``bel-commons manage load`` will automatically add the most recently exported
           user list
        3. ``bel-commons manage examples load`` will automatically load some example
           networks and data sets
        
        Citation
        --------
        If you find BEL Commons useful in your work, please consider citing [Hoyt2018]_ and [Hoyt2017]_:
        
        .. [Hoyt2018] Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). `BEL Commons: an environment for
                      exploration and analysis of networks encoded in Biological Expression Language
                      <https://doi.org/10.1093/database/bay126>`_. *Database*, 2018(3), 1–11.
        .. [Hoyt2017] Hoyt, C. T., Konotopez, A., & Ebeling, C., (2017). `PyBEL: a computational framework for Biological
                      Expression Language <https://doi.org/10.1093/bioinformatics/btx660>`_. *Bioinformatics*,
                      34(4), 703–704.
        
        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>`_
        - `IMI <https://www.imi.europa.eu/>`_ (in the `AETIONOMY <http://www.aetionomy.eu/>`_ project)
        
        Logo
        ~~~~
        The BEL Commons `logo <https://github.com/pybel/pybel-art>`_ was designed by `Scott Colby <https://github.com/scolby33>`_.
        
        .. |build| image:: https://travis-ci.com/bel-commons/bel-commons.svg?branch=master
            :target: https://travis-ci.com/bel-commons/bel-commons
            :alt: Travis-CI Build Status
        
        .. |docs| image:: https://readthedocs.org/projects/bel-commons/badge/?version=latest
            :target: https://bel-commons.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
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 :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.7
Provides-Extra: bio2bel
Provides-Extra: docs
