Project Name: wikipathways

Wikitech Usernames of requestors: Ariutta, AlexanderPico

Purpose: WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.

Brief description: Since 2008, WikiPathways has supported scientists from around the world in creating, sharing and analyzing biological pathway data, including COVID-related pathways. We have been working to further integrate our data with Wikimedia projects like Wikidata (paper) and Commons as well as additional third-party open data resources like NDEx in order to make our data more broadly available and useful.

We are using Toolforge for pathway-viewer and wikipathways2wiki. Toolforge is great for pathway-viewer (example), but it's not the best fit for wikipathways2wiki, because this project relies on specific versions of a large number of dependencies in multiple languages, not all of which are available for Toolforge. I was able to use Linuxbrew to make it work somewhat, but the number of kludges required makes in difficult to keep dev in sync with prod.

Sample software to install:

xmlstarlet

https://github.com/PathVisio/pathvisio
https://github.com/PathVisio/pathvisio/blob/master/LICENSE-2.0.txt

https://github.com/bridgedb/BridgeDb
https://github.com/bridgedb/BridgeDb/blob/master/LICENSE-2.0.txt

https://github.com/wikipathways/pvjs
https://github.com/wikipathways/pvjs/blob/master/LICENSE.txt

https://github.com/wikipathways/gpml2pvjson-js
https://github.com/wikipathways/gpml2pvjson-js/blob/master/LICENSE

How soon you are hoping this can be fulfilled: as soon as possible