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Debian To Take On COVID-19 With A Biohackathon

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Debian
Sci/Tech

Debian developers are wanting to do their part to take on the global coronavirus pandemic by hosting a COVID-19 Biohackathon.

This virtual event organized by Debian developers is taking place from 5 to 11 April. Their hope with this biohackathon is to "improve biomedical FOSS and the tools/libraries that support those projects."

Among the work they hope to see realized from this hackathon are addressing various bugs, contributing to upstream biomedical open-source software, and related work.

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Biohackathon: GNU/Linux Debian Join Hands To Fight COVID-19

  • Biohackathon: GNU/Linux Debian Join Hands To Fight COVID-19

    According to Telegraph, one-fifth of the world’s population is under lockdown in the fight against the COVID-19. Consequently, almost all domains of technology have come forward to help. Open-source giants like OpenSUSE have also started various initiatives to offer support for medical devices and tools.

    Along the same lines, yesterday, the open-source Debian Med team announced the launch of the online Biohackathon for students. The Med team also requested Debian developers to participate and contribute to improving biomedical free and open-source software.

Debian announces COVID-19 Biohackathon

  • Debian announces COVID-19 Biohackathon

    The Debian platform has many ‘Pure Blends’ available, which are distributions specifically designed to serve the requirements of a specific topic. For example, there is Ubuntu Studio, a version of Ubuntu, particularly for content creation. Or Fedora Labs.

    The team of Debian Med (medical-related Debian variation) has announced a ‘COVID-19 Biohackathon’ between 5 April and 11 April to help with the pandemic that has depredated the world.

Debian Calls the Linux World to Help Fight the New Coronavirus

  • Debian Calls the Linux World to Help Fight the New Coronavirus

    The idea of the online event is to bring the Linux world together in order to improve the way Debian can help the health industry fight against the new coronavirus, and Debian says anyone can contribute with bug triage, testing, documentation, CI, translations, packaging, and code contributions.

    “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 style,” the Debian developers explain.

Debian Linux readies an anti-coronavirus hack-a-thon

  • Debian Linux readies an anti-coronavirus hack-a-thon

    Open-source programmers and engineers have been working on a wide variety of projects to beat coronavirus. These range from hospital management programs to speeding up drug development to building inexpensive ventilators. Now, Debian Linux, one of the oldest and largest Linux distribution communities, is throwing its programming resources into beating COVID-19.

    The Debian Med team is inviting programmers to a virtual COVID-19 Biohackathon from April 5-11, 2020. The Debian Med team wants your help in improving free and open-source biomedical software programs, tools and libraries.

Debian @ COVID-19 Biohackathon (April 5-11, 2020)

  • Debian @ COVID-19 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
    style.
    
    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
    contribute.
    
    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
    
    [salsa-covid-19-bh20]
    https://salsa.debian.org/med-team/community/2020-covid19-...
    
    [robust-workflows] https://doi.org/10.1007/s41019-017-0050-4
    
    [cwltool-issues] https://github.com/common-workflow-language/cwltool/issues
    
    [COVID-19-advice]
    https://www.who.int/emergencies/diseases/novel-coronaviru...
    
    [debian-med-team-policy] https://med-team.pages.debian.net/policy/
    
    Sincerely,
    
    Michael R. Crusoe on behalf of the Debian-Med team
    
    (and Andreas Tille on behalf of Michael R. Crusoe ;-) )
    

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