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Challenges from and for the Bioconductor community

European Bioconductor Meeting 2020

Kevin Rue-Albrecht, Charlotte Soneson, Laurent Gatto, et EuroBioc2020 Organising Committee

2020-12-14 (updated: 2020-12-17)

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Community spirit

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The benefits of collaborations

  • Combine expertise to overcome issues.

  • Discuss and refine ideas.

  • Exposure to other perspectives
    (e.g., setup, workflow).

  • Share transferable skills and best practices
    (e.g., git, unit testing, CI/CD).

  • Gain experience with external collaborators.

  • Share the challenges and rewards of trying and working out an exciting idea together!

  • Connect with like-minded community members at all career stages.

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A (real) example

Once upon a EuroBioc conference, four postdocs sat together at a break.

Postdoc 1: "There's so much single-cell data out there... Always the same plots... Sometimes I wish we had a Shiny app to visualise any data stored in any SummarizedExperiment object."

Postdoc 2: "Me too! That would be so helpful to share with collaborators too!"

Postdoc 3: "Well, I've written a bunch of Shiny apps before. I'd love to help with that."

Postdoc 4: "Do you know about Shiny dashboards? Mind if I set up the app structure?"

Postdoc 2: (Opening up a laptop) "Alright, let me create a GitHub repository and add you."

Postdoc 3: "Great idea! Also, let's create a README and write out wish list of functionality."

Postdoc 1: "I'll create a Slack channel to keep the conversation going".

(By the end of the conference) SummarizedExplorer was born (and later renamed iSEE!).

See the initial README at https://github.com/iSEE/iSEE/tree/021e3e2

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What BiocChallenges is

  • A public platform for the Bioconductor community to announce and contribute to bite-sized projects beneficial to the community at all levels.

  • An R package (passes BiocCheck!)

  • Each vignette (under vignettes/challenges) represents a challenge.

  • Anyone can submit a new challenge (as a pull request).

  • Repositories contributing to the challenges are listed on the challenge page.

  • Each challenge is led by one or more volunteer (point of contact).

  • Ideally, challenges and contributions will lead to presentations, discussions, or workshops at Bioconductor events.

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What BiocChallenges is not

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A tour of BiocChallenges

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A tour of BiocChallenges

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A tour of BiocChallenges

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Work in progress

  • Your feedback is welcome.

    • Challenge format.

    • Additional information for each challenge.

    • Additional functionality.

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What can you do this week? (and beyond!)

Ideas

Check out existing challenges at https://kevinrue.github.io/BiocChallenges/.

Network and communicate.

Get in touch with like-minded participants and speakers.

Actions

Submit a pull request to add a challenge at https://github.com/kevinrue/BiocChallenges/

Contribute to an existing challenge repository.

Create new challenge repositories.

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At the end of this week

Friday 19:05 - 19:15 (CET)

BiocChallenges closing presentation


Notify me throughout the week, so that I can report new challenges, ideas, and contributions!

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References

Huber, W., V. J. Carey, et al. (2015NA). "Orchestrating high-throughput genomic analysis with Bioconductor". In: Nat Methods 12.2, pp. 115-21. ISSN: 1548-7105 (Electronic) 1548-7091 (Linking). DOI: 10.1038/nmeth.3252. URL: https://www.ncbi.nlm.nih.gov/pubmed/25633503.

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Community spirit

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