COVID-19 Biohackathon (5-11.4., 2020)

Es gibt einen Biohackathon vom 5.4. bis 11.4

Geht vor allem um Daten und Software. Dezentral und online soll er stattfinden.


Global COVID-19 Biohackathon Announced

March 27, 2020 — The ELIXIR & European Bioinformatics Communities are organizing the Global COVID-19 Biohackathon on April 5 – 11, 2020.

The goal of the biohackathon is to create a cohesive effort and work on tooling for COVID-19 analysis. This biohackathon will lead to more readily data accessibility, protocols, computational analysis tools, protein predictions etc. The participants will also push for policy change where it comes to non-public or hard to access data.

Anyone can join and contribute. This is a good opportunity for researchers in universities, universities of applied sciences and research institutions and CSC’s specialists to join forces, utilize their expertise and fight against the pandemic. Also, this provides Finnish researchers with a way to connect to global developer and data analyst community.

CSC participates in this hackathon by offering access to its state-of-the-art cloud computing and data lake services for hackathon participants.

  • cPouta IaaS cloud service access

  • Allas Object Storage service access

  • Rahti Container cloud service access

  • CWL workflow execution pipeline on Rahti*

  • Galaxy pulsar service via cPouta

  • under preparation

There are already over 150 participants globally who have registered for the hackathon. For new registrations, one needs to contact the organizing team. More information and contact details of the organising team are at GitHub - virtual-biohackathons/covid-19-bh20: COVID-19 Biohackathon April 5-11 2020.

About CSC

CSC – IT Center for Science is a Finnish center of expertise in information technology owned by the Finnish state and higher education institutions. We provide internationally high-quality ICT expert services for higher education institutions, research institutes, culture, public administration, and enterprises to help them thrive and benefit society at large.

Die Debian Community ist auch mit dabei.

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] Debian Med Covid-19 bugs

[covid-19-packages] Debian Med Covid-19 packages

[covid-19-bh20] GitHub - virtual-biohackathons/covid-19-bh20: COVID-19 Biohackathon April 5-11 2020

Debian Med / community / 2020-covid19-hackathon · GitLab


[cwltool-issues] Issues · common-workflow-language/cwltool · GitHub

Advice for public

[debian-med-team-policy] policy.rst


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

(and Andreas Tille on behalf of Michael R. Crusoe :wink: )

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