Challenges from and for the Bioconductor community

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# Challenges from and for the Bioconductor community <img src="img/sticker.png" height="150px">
## European Bioconductor Meeting 2020
### <a href="https://kevinrue.github.io">Kevin Rue-Albrecht</a>, <a href="https://csoneson.github.io">Charlotte Soneson</a>, <a href="https://lgatto.github.io">Laurent Gatto</a>, et <a href="https://eurobioc2020.bioconductor.org/organizing_committee">EuroBioc2020 Organising Committee</a>
### 2020-12-14 (updated: 2020-12-17)

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<div class="my-footer"><span>
Kevin Rue-Albrecht
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BiocChallenges
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# Community spirit

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# The benefits of collaborations

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- Combine expertise to overcome issues.

- Discuss and refine ideas.

- Exposure to other perspectives<br/>
  (e.g., setup, workflow).

- Share transferable skills and best practices<br/>
  (e.g., git, unit testing, CI/CD).
]

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<img src="img/minions-teamwork.png" style="display: block; margin: auto;" />
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- 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

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_Once upon a EuroBioc conference, four postdocs sat together at a break._
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**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

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- 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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<https://github.com/kevinrue/BiocChallenges>
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# A tour of BiocChallenges

.center[
<https://github.com/kevinrue/BiocChallenges>
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# A tour of BiocChallenges

.center[
<https://github.com/kevinrue/BiocChallenges>
]

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# Work in progress

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- Your feedback is welcome.

+ Challenge format.
  
  + Additional information for each challenge.
  
  + Additional functionality.
]
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<img src="img/minion-taking-notes.jpg" height="550px" style="display: block; margin: auto;" />
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# What can you do this week? (and beyond!)

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## Ideas
<i class="fab fa-github"></i> Check out existing challenges at <https://kevinrue.github.io/BiocChallenges/>.

<i class="far fa-comments"></i> Network and communicate.

- On the conference platform<br/>
  (e.g., booth, lounge, chat).<br/>
  _Also available outside live sessions._

- On the Bioconductor Slack at <https://community-bioc.slack.com>.

<i class="fas fa-user-friends"></i> Get in touch with like-minded participants and speakers.
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## Actions

<i class="fab fa-github"></i> Submit a pull request to add a challenge at
<https://github.com/kevinrue/BiocChallenges/>

<i class="fab fa-github"></i> Contribute to an existing challenge repository.

<i class="fab fa-github"></i> Create new challenge repositories.

<img src="img/minions-lets-go.jpg" style="display: block; margin: auto;" />
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# At the end of this week

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**Friday 19:05 - 19:15 (CET)**

**BiocChallenges closing presentation**
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<br/>

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

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# References

<a name=bib-orchestrating2015></a>[Huber, W., V. J. Carey, et
al.](#cite-orchestrating2015) (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](https://doi.org/10.1038%2Fnmeth.3252). URL:
[https://www.ncbi.nlm.nih.gov/pubmed/25633503](https://www.ncbi.nlm.nih.gov/pubmed/25633503).