Metadata-Version: 1.2
Name: pathme_viewer
Version: 0.0.8
Summary: A plugin for PathMe that allows to explore overlaps across pathway databases
Home-page: https://github.com/PathwayMerger/PathMe-Viewer
Author: Daniel Domingo-Fernández
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: Apache 2.0 License
Download-URL: https://pypi.org/project/pathme-viewer/
Description-Content-Type: UNKNOWN
Description: PathMe Viewer |build| |coverage| |docs| |zenodo|
        ================================================
        
        This web application aims to facilitate querying, browsing, and navigating pathway knowledge formalized in Biological
        Expression Language (BEL). While it was built paralelly with `PathMe <https://github.com/PathwayMerger/PathMe>`_, to
        facilitate the exploration of the databases harmonized by this package, the PathMe Viewer supports the visualization
        of BEL files.
        BEL files can be stored in the PathMe Viewer's database and so they queried in the main page. In this page, users can
        select multiple BEL files (pathways) to renders the corresponding merged network in a user-friendly visualization
        powered by multiple built-in functionalities.
        
        This web application is publicly accessible at http://pathme.scai.fraunhofer.de/ but can be locally deployed using
        Docker or PyPI (see Installation/Deployment sections).
        
        Citation
        --------
        If you use PathMe in your work, please cite [1]_:
        
        .. [1] Domingo-Fernández, D., *et al.* (2018). `PathMe: Merging and exploring mechanistic pathway knowledge
            <https://doi.org/10.1101/451625>`_. bioRxiv *451625*.
        
        How to Use
        ----------
        Exploring pathways through this web application is simple. First, select a set of pathways from different databases. To
        choose a pathway, first select a database and the autocompletion form will then guide you to find pathway(s) of
        interest to you. After pathways have been selected, click on the "Explore" button to render the merged network
        corresponding to the selected pathways.
        
        .. image:: https://github.com/PathwayMerger/PathMe-Viewer/blob/master/src/pathme_viewer/static/img/main_page_screenshot.jpg
            :width: 500px
        
        The resulting network is visualized in the next page where multiple functionalities enable the exploration of the
        pathway(s).
        
        .. image:: https://github.com/PathwayMerger/PathMe-Viewer/blob/master/src/pathme_viewer/static/img/visualization_example.jpg
            :width: 500px
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        PathMe can be installed easily from `PyPI <https://pypi.python.org/pypi/pathme>`_ running the following code in your
        terminal:
        
        .. code-block:: sh
        
            $ python3 -m pip install pathme_viewer
        
        or from the latest code on `GitHub <https://github.com/PathwayMerger/PathMe-Viewer>`_ with:
        
        .. code-block:: sh
        
            $ python3 -m pip install git+https://github.com/ComPath/PathMe-Viewer.git@master
        
        
        Database
        --------
        In order to visualize BEL files with the viwer, you have to load them into the databases. The following command to
        loads the databases converted to BEL by PathMe (note that the first time it runs might take a couple of hours).
        Additionally, users can customize the imports to other bel files or databases (please see the `documentation page
        <https://pathme-viewer.readthedocs.io/en/latest/>`_ ).
        
        .. code-block:: python
        
            python3 -m pathme_viewer manage load
        
        In order to check the status of the database, you can run:
        
        .. code-block:: python
        
            python3 -m pathme_viewer manage summarize
        
        The content of the database can be erased by running:
        
        .. code-block:: python
        
            python3 -m pathme_viewer manage drop
        
        Deployment
        ----------
        If you have already installed the PathMe-Viewer as a Python package and you have already populated the database, now
        you can deploy the web application by running:
        
        .. code-block:: python
        
            python3 -m pip install pathme_viewer web
        
        Note that the database runs by default in the following port: http://0.0.0.0:5000/. The Flask host and port can be
        modified by changing the default parameters (run: "python3 -m pathme_viewer web --help" for more info).
        
        Deployment of PathMe Viewer using Docker
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        To quickly deploy the web application locally, you can also use Docker. This can be achieved by running the following
        commands after installing Docker.
        
        1. Build a container named 'pathme' version 0.0.1 (you must be in the root directory after cloning this package with
           Git).
        
        .. code-block:: sh
        
            docker build -t pathme:0.0.1 .
        
        2. Run docker the pathme container version 0.0.1.
        
        .. code::
        
            docker run --name=pathme -d -p 5000:5000 --restart=always -d pathme:0.0.1
        
        Note: the docker file is meant to be run on http://127.0.0.1:5000/. If you want to change the host/port
        please modify dockerfile (line 55) and src/bin/bootstrap.sh (line 23).
        
        
        .. |build| image:: https://travis-ci.com/PathwayMerger/PathMe-Viewer.svg?branch=master
            :target: https://travis-ci.com/PathwayMerger/PathMe-Viewer
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/pathwaymerger/PathMe-Viewer/coverage.svg?branch=master
            :target: https://codecov.io/gh/pathwaymerger/PathMe-Viewer?branch=master
            :alt: Coverage Status
        
        .. |docs| image:: http://readthedocs.org/projects/pathme_viewer/badge/?version=latest
            :target: https://pathme_viewer.readthedocs.io/en/latest/
            :alt: Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/pathwaymerger/pathme_viewer/badges/gpa.svg
            :target: https://codeclimate.com/github/pathwaymerger/pathme_viewer
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/pathme_viewer.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/pathme_viewer.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/pathme_viewer.svg
            :alt: Apache-2.0
        
        .. |zenodo| image:: https://zenodo.org/badge/144898535.svg
           :target: https://zenodo.org/badge/latestdoi/144898535
        
Keywords: Pathway Databases,Systems Biology,Networks Biology,Biological Expression Language
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 :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
