pathme-viewer 0.0.6

Citation

If you use PathMe in your work, please cite:

Domingo-Fernández, D., et al. (2018). PathMe: Merging and exploring mechanistic pathway knowledge. 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.

The resulting network is visualized in the next page where multiple functionalities enable the exploration of the pathway(s).

Installation

PathMe can be installed easily from PyPI running the following code in your terminal:

$ python3 -m pip install pathme_viewer

or from the latest code on GitHub with:

$ 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 ).

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

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:

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).

docker build -t pathme:0.0.1 .

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