{
    "info": {
        "author": "Daniel Domingo-Fern\u00e1ndez",
        "author_email": "daniel.domingo.fernandez@scai.fraunhofer.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "PathMe Viewer |build| |coverage| |docs| |zenodo|\n================================================\n\nThis web application aims to facilitate querying, browsing, and navigating pathway knowledge formalized in Biological\nExpression Language (BEL). While it was built paralelly with `PathMe <https://github.com/PathwayMerger/PathMe>`_, to\nfacilitate the exploration of the databases harmonized by this package, the PathMe Viewer supports the visualization\nof BEL files.\nBEL files can be stored in the PathMe Viewer's database and so they queried in the main page. In this page, users can\nselect multiple BEL files (pathways) to renders the corresponding merged network in a user-friendly visualization\npowered by multiple built-in functionalities.\n\nThis web application is publicly accessible at http://pathme.scai.fraunhofer.de/ but can be locally deployed using\nDocker or PyPI (see Installation/Deployment sections).\n\nCitation\n--------\nIf you use PathMe in your work, please cite [1]_:\n\n.. [1] Domingo-Fern\u00e1ndez, D., *et al.* (2018). `PathMe: Merging and exploring mechanistic pathway knowledge\n    <https://doi.org/10.1101/451625>`_. bioRxiv *451625*.\n\nHow to Use\n----------\nExploring pathways through this web application is simple. First, select a set of pathways from different databases. To\nchoose a pathway, first select a database and the autocompletion form will then guide you to find pathway(s) of\ninterest to you. After pathways have been selected, click on the \"Explore\" button to render the merged network\ncorresponding to the selected pathways.\n\n.. image:: https://github.com/PathwayMerger/PathMe-Viewer/blob/master/src/pathme_viewer/static/img/main_page_screenshot.jpg\n    :width: 500px\n\nThe resulting network is visualized in the next page where multiple functionalities enable the exploration of the\npathway(s).\n\n.. image:: https://github.com/PathwayMerger/PathMe-Viewer/blob/master/src/pathme_viewer/static/img/visualization_example.jpg\n    :width: 500px\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\nPathMe can be installed easily from `PyPI <https://pypi.python.org/pypi/pathme>`_ running the following code in your\nterminal:\n\n.. code-block:: sh\n\n    $ python3 -m pip install pathme_viewer\n\nor from the latest code on `GitHub <https://github.com/PathwayMerger/PathMe-Viewer>`_ with:\n\n.. code-block:: sh\n\n    $ python3 -m pip install git+https://github.com/ComPath/PathMe-Viewer.git@master\n\n\nDatabase\n--------\nIn order to visualize BEL files with the viwer, you have to load them into the databases. The following command to\nloads the databases converted to BEL by PathMe (note that the first time it runs might take a couple of hours).\nAdditionally, users can customize the imports to other bel files or databases (please see the `documentation page\n<https://pathme-viewer.readthedocs.io/en/latest/>`_ ).\n\n.. code-block:: python\n\n    python3 -m pathme_viewer manage load\n\nIn order to check the status of the database, you can run:\n\n.. code-block:: python\n\n    python3 -m pathme_viewer manage summarize\n\nThe content of the database can be erased by running:\n\n.. code-block:: python\n\n    python3 -m pathme_viewer manage drop\n\nDeployment\n----------\nIf you have already installed the PathMe-Viewer as a Python package and you have already populated the database, now\nyou can deploy the web application by running:\n\n.. code-block:: python\n\n    python3 -m pip install pathme_viewer web\n\nNote that the database runs by default in the following port: http://0.0.0.0:5000/. The Flask host and port can be\nmodified by changing the default parameters (run: \"python3 -m pathme_viewer web --help\" for more info).\n\nDeployment of PathMe Viewer using Docker\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nTo quickly deploy the web application locally, you can also use Docker. This can be achieved by running the following\ncommands after installing Docker.\n\n1. Build a container named 'pathme' version 0.0.1 (you must be in the root directory after cloning this package with\n   Git).\n\n.. code-block:: sh\n\n    docker build -t pathme:0.0.1 .\n\n2. Run docker the pathme container version 0.0.1.\n\n.. code::\n\n    docker run --name=pathme -d -p 5000:5000 --restart=always -d pathme:0.0.1\n\nNote: the docker file is meant to be run on http://127.0.0.1:5000/. If you want to change the host/port\nplease modify dockerfile (line 55) and src/bin/bootstrap.sh (line 23).\n\n\n.. |build| image:: https://travis-ci.com/PathwayMerger/PathMe-Viewer.svg?branch=master\n    :target: https://travis-ci.com/PathwayMerger/PathMe-Viewer\n    :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/pathwaymerger/PathMe-Viewer/coverage.svg?branch=master\n    :target: https://codecov.io/gh/pathwaymerger/PathMe-Viewer?branch=master\n    :alt: Coverage Status\n\n.. |docs| image:: http://readthedocs.org/projects/pathme_viewer/badge/?version=latest\n    :target: https://pathme_viewer.readthedocs.io/en/latest/\n    :alt: Documentation Status\n\n.. |climate| image:: https://codeclimate.com/github/pathwaymerger/pathme_viewer/badges/gpa.svg\n    :target: https://codeclimate.com/github/pathwaymerger/pathme_viewer\n    :alt: Code Climate\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pathme_viewer.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/pathme_viewer.svg\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/pathme_viewer.svg\n    :alt: Apache-2.0\n\n.. |zenodo| image:: https://zenodo.org/badge/144898535.svg\n   :target: https://zenodo.org/badge/latestdoi/144898535",
        "description_content_type": "",
        "docs_url": null,
        "download_url": "https://pypi.org/project/pathme-viewer/",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/PathwayMerger/PathMe-Viewer",
        "keywords": "Pathway Databases,Systems Biology,Networks Biology,Biological Expression Language",
        "license": "Apache 2.0 License",
        "maintainer": "Daniel Domingo-Fern\u00e1ndez",
        "maintainer_email": "daniel.domingo.fernandez@scai.fraunhofer.de",
        "name": "pathme-viewer",
        "package_url": "https://pypi.org/project/pathme-viewer/",
        "platform": "",
        "project_url": "https://pypi.org/project/pathme-viewer/",
        "project_urls": {
            "Bug Tracker": "https://github.com/PathwayMerger/PathMe-Viewer/issues",
            "Documentation": "https://pathme-viewer.readthedocs.io/en/latest/",
            "Download": "https://pypi.org/project/pathme-viewer/",
            "Homepage": "https://github.com/PathwayMerger/PathMe-Viewer",
            "Source Code": "https://github.com/PathwayMerger/PathMe-Viewer"
        },
        "release_url": "https://pypi.org/project/pathme-viewer/0.0.9/",
        "requires_dist": null,
        "requires_python": ">=3.6",
        "summary": "A plugin for PathMe that allows to explore overlaps across pathway databases",
        "version": "0.0.9"
    },
    "last_serial": 4943497,
    "releases": {
        "0.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "4ef267343945325a14d76a9dabecb0d2",
                    "sha256": "573da14459e619d53f3221209a86f347701bd57e62cd40d5af4be5b27724c921"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "4ef267343945325a14d76a9dabecb0d2",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 15433,
                "upload_time": "2018-10-10T12:09:16",
                "url": "https://files.pythonhosted.org/packages/23/78/9b8b2000199e18a01f910441dd62d7d74814f26df66c916625110462ebf8/pathme_viewer-0.0.1.tar.gz"
            }
        ],
        "0.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "3155ff876f72c4d769724325e83438ff",
                    "sha256": "9bd31ce2956b01f382aff2a34ba42ab045ad217513f7f54422eb520d2992aa46"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "3155ff876f72c4d769724325e83438ff",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 15917,
                "upload_time": "2018-10-19T07:46:13",
                "url": "https://files.pythonhosted.org/packages/f9/64/85ea30284c8c4168c4a0318173913e5036f6c7a85c7e18c296e7a5f84ac8/pathme_viewer-0.0.2.tar.gz"
            }
        ],
        "0.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f945d69f4481dc578592b1f2aa57b42b",
                    "sha256": "a95081393e61f4b30db8c50c05468770566a9bb9476819d8388572e606bf06b1"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "f945d69f4481dc578592b1f2aa57b42b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 16317,
                "upload_time": "2018-10-22T22:31:04",
                "url": "https://files.pythonhosted.org/packages/a2/96/cf1c52f2cc25e18b3863547f1cae34a8b84b9761a7b11a994a5dbd08170a/pathme_viewer-0.0.3.tar.gz"
            }
        ],
        "0.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "3da7b572d4b68936af320b046160e5bc",
                    "sha256": "1b016826e656bb49df9f320cbd0d194de96f3d967f06b1f0098b8aa49afe11a7"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "3da7b572d4b68936af320b046160e5bc",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 19475,
                "upload_time": "2018-12-07T10:31:08",
                "url": "https://files.pythonhosted.org/packages/31/65/660ddfb13eec8ec92606b5b1228a0d3cee5475184c557bfaf2571d35e333/pathme_viewer-0.0.4.tar.gz"
            }
        ],
        "0.0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "fb6a3a76513a4801e461e60ce0c6c9d8",
                    "sha256": "b106a1c2b453df01443da4db4b38ec09c0fe34b0fc5118b3ce134c385f5b69c3"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "fb6a3a76513a4801e461e60ce0c6c9d8",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 19474,
                "upload_time": "2018-12-07T10:32:00",
                "url": "https://files.pythonhosted.org/packages/b7/e3/9bf7a762b697327014a62da683b5636889979f196a9677c8c3f7b8bb5da5/pathme_viewer-0.0.5.tar.gz"
            }
        ],
        "0.0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "29184df5d8548e48063b90ef3271fc5b",
                    "sha256": "f60de5e9e0ee0adfc4b8d58911f1793b33bcf8499004eac412a4f2f3f40fbb75"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "29184df5d8548e48063b90ef3271fc5b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 739409,
                "upload_time": "2018-12-07T10:59:32",
                "url": "https://files.pythonhosted.org/packages/c3/8c/17d36ccbe8d10071819117ece53df39d4141bccd0d16b0f90f89a3c89fe9/pathme_viewer-0.0.6.tar.gz"
            }
        ],
        "0.0.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "bb8c4372793b76a57325a05cfff959de",
                    "sha256": "cfe321cd0324aaa4672981c52a3368ed818676860b536ab5cf697ed7e989681e"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.7.tar.gz",
                "has_sig": false,
                "md5_digest": "bb8c4372793b76a57325a05cfff959de",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 761268,
                "upload_time": "2019-01-16T20:37:02",
                "url": "https://files.pythonhosted.org/packages/c4/c5/30ff22225a28f3182e2245600d278f87096b755e107024c1f8c6772bed27/pathme_viewer-0.0.7.tar.gz"
            }
        ],
        "0.0.8": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "48ca079ea9e7e76563999f64f73970f2",
                    "sha256": "18a02acf2be2d326338af572437391ba78f6a5589a6ee9a6975fce6595fca679"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.8.tar.gz",
                "has_sig": false,
                "md5_digest": "48ca079ea9e7e76563999f64f73970f2",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 745289,
                "upload_time": "2019-03-13T21:39:36",
                "url": "https://files.pythonhosted.org/packages/44/c8/bba793285fb32e5e8fceb4be99ec289c64c65da57546f7aff68bee55c906/pathme_viewer-0.0.8.tar.gz"
            }
        ],
        "0.0.9": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ca8d01cb03fbbea9c2b494f3edd6f140",
                    "sha256": "674a0255a980fc6b5410380fdaf2ef0be58cf4290e2dc5e327922a7378420eef"
                },
                "downloads": -1,
                "filename": "pathme_viewer-0.0.9.tar.gz",
                "has_sig": false,
                "md5_digest": "ca8d01cb03fbbea9c2b494f3edd6f140",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 745967,
                "upload_time": "2019-03-15T10:05:33",
                "url": "https://files.pythonhosted.org/packages/15/b1/86690d51c6e2bc87721011440c8bb2c6a3d771565131f2d793c4b2d8d725/pathme_viewer-0.0.9.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "ca8d01cb03fbbea9c2b494f3edd6f140",
                "sha256": "674a0255a980fc6b5410380fdaf2ef0be58cf4290e2dc5e327922a7378420eef"
            },
            "downloads": -1,
            "filename": "pathme_viewer-0.0.9.tar.gz",
            "has_sig": false,
            "md5_digest": "ca8d01cb03fbbea9c2b494f3edd6f140",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6",
            "size": 745967,
            "upload_time": "2019-03-15T10:05:33",
            "url": "https://files.pythonhosted.org/packages/15/b1/86690d51c6e2bc87721011440c8bb2c6a3d771565131f2d793c4b2d8d725/pathme_viewer-0.0.9.tar.gz"
        }
    ]
}