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For people interested in FOSS (and I'm sure some o...
# shameless-promo
a
For people interested in FOSS (and I'm sure some of you are !), we would like to create a space for bioinformatics in next year FOSDEM (European FOSS conference). Nf-core pipeline would be a great fit for that ! If you are even remotely interested in doing a talk, let me know in PM. There's nothing definitive as we'll aim for a proposal first 🙂
n
I love this idea! Do you have any idea yet when the next edition would take place?
a
There’s no official date but I’ve heard it could be on February 2nd
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n
I can't commit fully yet without knowing exactly when it would take place but I'm definitely interested in representing nf-core 🙂
a
That would be awesome. Thanks !
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n
Keep me updated 😉
a
Of course :)
p
Ace! FOSDEM has been on my radar for a while, I think that there are also some folks in Seqera who love the event ( @Lorenzo Fontana ?)
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l
omg yes, let's do that. @Nicolas Vannieuwkerke historically it happens the first weekend of February so I would expect 7-8. It's always on a weekend.
n
Perfect, I can make time on that weekend 😛
c
There's a long running HPC dev room... https://fosdem.org/2025/schedule/track/hpc/ Happy to make an introduction to the folks organising it. Either to have you blend in for 2026 to tip your toe into the FOSDEM community OR get some advise on how to create your own (and what pitfalls to avoid).
a
@Christian Kniep thanks for the advice. There is definitely some overlap but there are other things to be said for bioinformatics too. I would love to be in touch with the people from HPC if possible :)
@Christian Kniep Hi, just pinging you as I would like to get in touch with the guys organizing the HPC room. Thanks 🙂
n
The event seems to be happening on the 31st of January and the 1st of February 😛. Any updates on the room?
a
We submitted the proposal. I’ll let you know if it’s accepted or not !
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It should be announced on October 26th
n
Awesome! Fingers crossed 🤞
c
Dear all, I was just contacted by Alessandro Pilotti who will be running the Bioinformatics & Computational Biology track, the deadline in on the 16/11. He was asking me if any of us would be interested with this specific track
a
Hi all, replying here to be sure it’s the proper place. Our dev room has been accepted and are looking for talks. So if anyone from Nextflow, nf-core want to submit a talk, please go to https://pretalx.fosdem.org/fosdem-2026/cfp. If it isn’t clear or if you have any question, let us know !
p
I'm not really familiar with how FOSDEM works. Are these two separate things? 👆
n
I'd be happy to present nf-core, I'll submit a proposal next week
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a
@Phil Ewels FOSDEM is the conference with several rooms. One of them is about bioinformatics. You submit a talk in the appropriate room :)
@Nicolas Vannieuwkerke awesome !
n
Any pointers on this as the abstract?
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The nf-core initiative is a global, open-source community dedicated to developing high-quality, portable, and reproducible bioinformatics pipelines built using Nextflow. Since its inception, nf-core has set rigorous standards for documentation, testing, versioning and packaging of workflows, ensuring that pipelines can be "run anywhere" with confidence. This talk will explore how to use these best-practice pipelines and how to leverage the tooling to easily create pipelines using the nf-core framework.
(I'm not the best writer so please point out any issues, even the smallest things will help a lot 😛, I also used chatGPT quite heavily 😁)
a
One major pro of nf-core is its set of “reference “ pipelines for many analysis. You could stress the best-practice part :) I think the audience could be interested in knowing if their homemade pipeline can be replaced by nf-core, the pros and the cons :)
And maybe lay out how the talk is structured ? E.g are you talking about the architecture of a typical pipeline, criteria for accepting a new pipeline, adoption …
n
Thank you! These are good points, I'll update the draft 😉
The talk will mainly be about using nf-core pipelines and a small bit about creating pipelines with the nf-core tooling. Is there something else you would really love to be in it or does this look good to you? The using the pipelines part will of course also explain how to find pipelines relevant the audience
a
PS: sorry if my reply was a bit short, I was writing on the phone
n
No worries, we still have lots of time 😛
a
Personally, I would love to have some real feedback about the follow-up of pipelines (maintenance burden) : do people just use the pipelines or do they fork it ? If that's the case, how do they keep-up with upstream. But that's just for me
If you have some data about updates (to show it's well maintained or not -- I was disappointed by the nanopore pipeline), and adoption (how many people use it and for what), that would be cool
And maybe talk about the community effort ? The hackathon for example
n
I will definitely mention community effort, I'm not sure pipeline maintenance is something that should be in an introduction talk as this is pretty technical already, but feel free to come up to me at the event and we can talk about this at length 😛. (Or ask it during the Q&A part)
a
You're right ! But if you have some "success stories" that would help convince the audience 🙂
n
Good point, I'll think about it 🤔
I'll send you another version of the draft once finished
a
Perfect ! If you have other people than want to talk about a specific pipeline, that could be in another talk too
n
Good idea, feel free to ask some people from the community to gauge the interest 😛
a
Done !
n
Perfect 😛
How about this?
Copy code
The nf-core initiative is a global, open-source community dedicated to developing high-quality, portable, and reproducible bioinformatics pipelines built using Nextflow. Since its inception, nf-core has set rigorous standards for documentation, testing, versioning and packaging of workflows, ensuring that pipelines can be "run anywhere" with confidence. This talk will be a short introduction to nf-core in which you will learn what the nf-core community is, how to use the pipelines, how you can use the nf-core tooling to create best-practice pipelines yourself all explained using applicable examples.
a
Works for me !
If you can give us a ideal duration, it would help as well
n
Yes I put it in the title 🙂 I'll submit the proposal
I put it in the submission notes now
a
It's in the review queue, thanks. Don't hesitate to spread the word if you know other people
n
Thanks 😛 I'll think about who would be interested! Maybe @Joon Klaps as he is about to release an nf-core pipeline 😛
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m
🚀
j
Hi! We were discussing about this conference in the lab and I thought that it would be good to present nf-core/tools if you think that it fits the scope 🙂
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@Nicolas Vannieuwkerke I don't think it would be too overlapping with your talk, right?
n
Oh not at all, I'll just focus on the other aspects of the community then 😛
a
@Júlia Mir I was suggesting that to Nicolas. Please submit a talk if you can !
j
ok thanks! I will submit an abstract 🙂
j
Related to @Júlia Mir comment we also discuss in the lab that we could present one of the pipelines we are maintaining in the lab #C0351A8S487 and the idea is to present it and its community driven development and maintainance
party this 3
a
Thanks ! You can add an ideal talk duration in your proposal if possible. We have 5, 10 or 20min + questions
@Júlia Mir @Nicolas Vannieuwkerke thanks again for your submissions ! We had more talks than expected and have to cut down a few corners. Would you be okay to do a joint presentation (10min each so 20 min in total + 5min questions) ? Sorry about that !
n
No worries, this sounds good to me! Still plenty of time to talk about nf-core 😉
j
ok, we can coordinate. should we change the abstract & title?
a
Perfect ! Choosing une submission and updating it would be great
n
We can use yours @Júlia Mir, you can add me and I will migrate my part of the proposal to yours 🙂
a
Could you ping me when it's ready ? Thanks 🙂
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a
Great! @Júlia Mir @Nicolas Vannieuwkerke, beside the joint talk (thank you for accepting to merge your talks BTW!), would you guys like to have some sort of informal mini community event (aka meeting for beers) around nf-core in the evening after the devroom talks? I think quite a few people could be interested
n
That sounds good to me, what would you expect from us for that?
a
Nothing complicated from a logistical standpoint: just being around and chat with people interested in nf-core, if you have time and you’d like to! In case it would be great to mention it at the end of you talk. It can even be as simple as hanging out somewhere onsite, e.g., near the campus cafeteria, we can define the details later.
Additionally, we are looking into organizing a gathering of the Bioinformatics devroom after the event downtown in the evening, so this could simply be part of it. Last but not least, there’s also the option of doing a BoF about nf-core if you guys would prefer something slightly more formal
n
Just being there to have a chat is perfectly fine, I can stay until the second to last train leaves 🙂
I'm not sure we would need something more formal, especially for the first time
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a
Perfect, thanks! 🙂
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j
an nf-core focused small event sounds good! @Jose Espinosa-Carrasco will also be there so can help aswell. thansk for the ofer 🙂
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j
Yes, happy to be involved 😃
n
@Alexis Praga we updated Julia's proposal :)
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And I've withdrawn mine
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