Home TECHNOLOGY COVID-19: Debian Biohackathon

COVID-19: Debian Biohackathon

April 5-11, 2020

Dear Debian Community,

There will be an virtual (online) COVID-19 Biohackathon from April 5-11,
2020 and the Debian Med team invite you help us improve biomedical FOSS
and the tools/libraries that support those projects.

Most tasks do not require any knowledge of biology or medicine, and all
types of contributions are welcome: bug triage, testing, documentation,
CI, translations, packaging, and code contributions.

1. Debian related bugs are viewable at [covid19-bugs]

2. Software awaiting packaging is listed at [covid-19-packages], please
respond to the RFP with your intent so we don't duplicate work

3. You can also contribute directly to the upstream packages, linked
from the Debian Med COVID-19 task page at [covid-19-packages]. Note:
many biomedical software packages are quite resource limited, even
compared to a typical FOSS project. Please be kind to the upstream
author/maintainers and realize that they may have limited resources to
review your contribution. Triaging open issues and opening pull requests
to fix problems is likely to be more useful than nitpicking their coding

4. Architectures/porting: Please focus on amd64, as it is the primary
architecture for biomedical software. A secondary tier would be arm64 /
ppc64el / s390x (but beware the endian-related issues on s390x). From a
free/open hardware perspective it would be great to see more riscv64
support, but that is not a priority right now

5. The Debian Med team is also trying to improve the availability of
automated biomedical pipelines/workflows [robust-workflows] using the
Common Workflow Language open standard. The reference implementation of
CWL is written in Python and there are many open issues ready for work
that don't require any biomedical background [cwltool-issues]

6. It is very easy to contribute to Debian Med team. We have a lowNMU
policy for all our packages. Merge requests on Salsa are usually
processed quickly (but please ping some of the latest Uploaders of the
package to make sure it will be noticed). Even better if you ask for
membership to the team and push directly to the salsa repository.

7. The [debian-med-team-policy] should answer all questions how to

The main COVID-19 biohackathon is being organized at [covid-19-bh20] and
for Debian's participation we are using [salsa-covid-19-bh20]

[covid-19-bugs] https://blends.debian.org/med/bugs/covid-19.html

[covid-19-packages] https://blends.debian.org/med/tasks/covid-19

[covid-19-bh20] https://github.com/virtual-biohackathons/covid-19-bh20


[robust-workflows] https://doi.org/10.1007/s41019-017-0050-4

[cwltool-issues] https://github.com/common-workflow-language/cwltool/issues


[debian-med-team-policy] https://med-team.pages.debian.net/policy/


Michael R. Crusoe on behalf of the Debian-Med team

(and Andreas Tille on behalf of Michael R. Crusoe ;-) )



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