Package: pathme-viewer
This web application aims to facilitate querying, browsing, and navigating pathway knowledge formalized in Biological
Expression Language (BEL). While it was built paralelly withPathMe, 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 athttp://pathme.scai.fraunhofer.de/but can be locally deployed using
Docker or PyPI (see Installation/Deployment sections).CitationIf you use PathMe in your work, please cite[1]:[1]Domingo-Fernández, D.,et al.(2018).PathMe: Merging and exploring mechanistic pathway knowledge. bioRxiv451625.How to UseExploring 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).InstallationPathMe can be installed easily fromPyPIrunning the following code in your
terminal:$python3-mpipinstallpathme_vieweror from the latest code onGitHubwith:$python3-mpipinstallgit+https://github.com/ComPath/PathMe-Viewer.git@masterDatabaseIn 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 thedocumentation page).python3-mpathme_viewermanageloadIn order to check the status of the database, you can run:python3-mpathme_viewermanagesummarizeThe content of the database can be erased by running:python3-mpathme_viewermanagedropDeploymentIf 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-mpipinstallpathme_viewerwebNote 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 DockerTo quickly deploy the web application locally, you can also use Docker. This can be achieved by running the following
commands after installing Docker.Build a container named ‘pathme’ version 0.0.1 (you must be in the root directory after cloning this package with
Git).dockerbuild-tpathme:0.0.1.Run docker the pathme container version 0.0.1.docker run --name=pathme -d -p 5000:5000 --restart=always -d pathme:0.0.1Note: the docker file is meant to be run onhttp://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).