The Best Covid-19 Projects on GitHub

The amount of attention that Covid-19 got last week increased dramatically, and that is a good thing.  An unfortunate casualty is that the quality of the average discussion of the virus dropped as the story-of-the-day journalists piled into coverage.  My twitter feed was getting stale and repetitive, so as an experiment I tried to see what coronavirus projects were up on GitHub.  Here are the top finds.

1.  Johns Hopkins Dashboard

The source data and code for the much-linked Johns Hopkins dashboard is here.  There is also a coronavirus package for R that makes it easy to pull the Johns Hopkins data, and looks to provide the plumbing behind many of the "days behind Italy" that were everywhere last week.

I would still love to see a public dataset on confirmed and suspected cases at a more granular level, preferably by city block like the map available for Singapore.

2. Wolfram Language code and notebooks related to the coronavirus outbreak

Example code for maps, animated charts (flattening the curve is that much better when you can see it move), images, and web scraping from Wolfram.  And here is the Wolfram community page.

3. Folding@Home

"Folding@home (FAH or F@h) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics."  I've literally never heard of them before this weekend.  Here is their wiki and their website.  Their GitHub page covering their Covid-19 efforts is here (of less practical use, unless of course you are deep in the weeds on protein folding and computational drug design).  Donating some processing power seems like an easy and say way to contribute to efforts to combat the virus, and you can start folding here.

4.  Nextstrain

"Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data."  The GitHub page for this one is also going to be for a pretty limited audience, but it is here.  According to their website, the project has sequenced over 500 samples of Covid-19.  I recommend this interview with computational biologist/co-developer Trevor Bedford, who happens to be at Fred Hutch in Seattle.