Over the internet we are organizing the COVID-19 Biohackathon April 5-11 2020!
The goal of COVID-19-BH20 is to create a cohesive effort and work on tooling for COVID-19 analysis. The biohackathon will lead to more readily accessible data, protocols, detection kits, protein predictions etc.
We will also push for policy change where it comes to non-public or hard to access data because we are facing such challenges!
Free software, free data
The biohackathon is about applying free and open source software on open data for scientific endeavour and biomedical progress.
The biohackathon wil run from April 5th-11th 2020. Before that time working groups will start preparations. After the biohackathon collaborations often continue.
Over the internet we are forming groups with topics to work on. There will be working groups for FAIR data, workflows and pipelines, pangenomes and variation graphs, machine learning, text mining and visualisations. You can create your own group and get people interested in your area of work. We will use video conferencing, E-mail, IRC, messaging, wiki's and source code repositories to make it all happen.
A concrete outcome is that if someone sequences a new patient they should be able to immediately compare it with all other known strains in a variation graph/pangenome. Standardized FAIR (metadata) and public repositories of (raw) data - that people can contribute to - as well as workflows that can be run by anyone (in the cloud) are all concrete outcomes.
The following wiki page lists known resources.
Anyone can join and contribute. Thanks to the annual biohackathons in Japan and Europe we already have an experienced community. One benefit of this virtual biohackathon is that we can expand and be as inclusive as possible. Even if you are a student and not so experienced you can sign-up and contribute! All hands are welcome!
We will organize goals and mini-publications for each group. Contributors will get credit for work.
Code of conduct
Anyone participating agrees to abide by the code of conduct as given by Code of Conduct. Please bring any concerns to the immediate attention of our coordinating team:
- Pjotr Prins, USA (pjotr.public708 at thebird.nl)
- Tazro Ohta, Japan (t.ohta at dbcls.rois.ac.jp)
- Leyla Garcia, Germany (ljgarciaco at gmail.com)
Contribute by adding and/or signing up to ideas on the Biohackathon Wiki. You can also edit these pages and send a pull request.
Sign up with the mailing list and ask!
- ELIXIR Europe and Galaxy have kindly agreed to provide computing resources
- Slack has kindly provided the full Slack version free of charge for up to 90 days.
- Curii Corporation has provided engineering time to setup the biohackathon.curii.com instance of the Arvados workflow platform.
- Amazon AWS for cloud credits to power biohackathon.curii.com