Skip to main content

A plugin for PathMe that allows to explore overlaps across pathway databases.

Project description

This plugin initializes the pathway viewer in ComPath that allows to explore overlaps between pathways using the canonical mappings.

Installation Current version on PyPI Stable Supported Python Versions Apache-2.0

  1. pathme_viewer can be installed with the following commands:

$ python3 -m pip install git+
  1. or in editable mode with:

$ git clone
$ cd PathMe-Viewer
$ python3 -m pip install -e .


The web application requires to load the pathways from the databases in the BEL. Thus, it is required to the following command to load the database (note that the first time it runs might take a couple of hours).

python3 -m pathme_viewer manage load

In order to check the status of the database, you can run:

python3 -m pathme_viewer manage summarize

The content of the database can be erased by running:

python3 -m pathme_viewer manage drop


Once the desired pathway databases are loaded, you can deploy the web application by running:

python3 -m pip install pathme_viewer web

Note that the database runs by default in the following port: 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 ComPath with Docker

  1. Build the container named ‘pathme’ version 0.0.1.

docker build -t pathme:0.0.1 .
  1. Run docker the pathme container version 0.0.1.

docker run --name=pathme -d -p 5000:5000 --restart=always -d pathme:0.0.1

How to Use

Here is an example of the visualization of Apoptosis equivalent pathways.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pathme_viewer-0.0.2.tar.gz (15.9 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page