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Christian Meesters
Christian Meesters
@rupdecat@fediscience.org  ·  activity timestamp 2 weeks ago

The last blog post I wrote was about Life Science Support on HPC clusters. Honestly? It was more of a rant. Not a good blog post.

So, someone suggested I delete it, which I did. It took me a long time to recover. Now, I have re-written this blog post. I think it is better. I weighted every phrase. It still has some rant flavour.

Here it is: https://blogs.fediscience.org/rupture-de-catenaire/2025/12/15/empowering-life-scientists-what-hpc-support-should-look-like/

The upcoming articles will have more of an example character. But I still will not be able to update on a regular basis.

#Bioinformatics #HPC #ReproducibleComputing #Snakemake #Nextflow

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Christos Argyropoulos MD PhD
Christos Argyropoulos MD PhD
@ChristosArgyrop@mastodon.social  ·  activity timestamp 3 weeks ago

David Condon just released a #NextFlow/ #snakemame pipeline/logger alternative in #Perl:

https://metacpan.org/pod/SimpleFlow

which should make debugging and running very complex #pipelines much easier.

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Egon Willigh☮gen 🟥 boosted
Pierre Lindenbaum
Pierre Lindenbaum
@yokofakun@genomic.social  ·  activity timestamp last month

new to me: "Data Lineage" in #nextflow

https://nextflow.io/docs/latest/tutorials/data-lineage.html

"Data lineage in Nextflow provides comprehensive tracking of workflow runs, task executions, and output files. This feature helps you verify the integrity and reproducibility of your pipeline results by maintaining a complete history of computations and intermediate data."

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Pierre Lindenbaum
Pierre Lindenbaum
@yokofakun@genomic.social  ·  activity timestamp last month

new to me: "Data Lineage" in #nextflow

https://nextflow.io/docs/latest/tutorials/data-lineage.html

"Data lineage in Nextflow provides comprehensive tracking of workflow runs, task executions, and output files. This feature helps you verify the integrity and reproducibility of your pipeline results by maintaining a complete history of computations and intermediate data."

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Konrad Förstner 💻🧬🦠 boosted
NFDI4Microbiota
NFDI4Microbiota
@NFDI4Microbiota@nfdi.social  ·  activity timestamp 2 months ago

🧬 Weekly #Nextflow & #nfcore Drop-in Session!
Got questions about your workflows? Need help building or running pipelines?

💬 Join our open session this Friday 10–11 CET with Daniel Straub (Uni Tübingen) — no registration needed!

📍 Zoom:https://tinyurl.com/mwz84xvb
#Bioinformatics #FAIRdata #OpenScience #NFDI4Microbiota

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NFDI4Microbiota
NFDI4Microbiota
@NFDI4Microbiota@nfdi.social  ·  activity timestamp 2 months ago

🧬 Weekly #Nextflow & #nfcore Drop-in Session!
Got questions about your workflows? Need help building or running pipelines?

💬 Join our open session this Friday 10–11 CET with Daniel Straub (Uni Tübingen) — no registration needed!

📍 Zoom:https://tinyurl.com/mwz84xvb
#Bioinformatics #FAIRdata #OpenScience #NFDI4Microbiota

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Christian Meesters
Christian Meesters
@rupdecat@fediscience.org  ·  activity timestamp 2 months ago

@mario_angst_sci honestly, it depends on what you mean by "data science":
- these days there are people who spell "data science" and mean #AI 🙄
- on a more serious note, there is the different library ecosystem of R and Python. This is mostly domain-specific. Both, as you know, are pretty generic, until you meet a certain domain (e.g. imputation methods or biological analysis), where one or the other excels.
- Speaking about EXCEL, you might want to drop in https://datavzrd.github.io/ - a viable alternative.
- If you really want to go nuclear, teach workflow management systems ( #Snakemake, #Nextflow). 😉

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Shauna GM
Shauna GM
@shauna@social.coop  ·  activity timestamp 4 months ago

Are you part of an open source project with a community of users, contributors, and/or third party developers?

I want to interview people about their projects with particular attention to how codebases, documentation, project management tooling, and community spaces are constructed.

On these "project tours" we'll go through your project together, on video call, and talk about how the structure of the project influences, and is influenced by, your goals, culture, logistical constraints, etc.

Maxime Garcia
Maxime Garcia
@gau@scholar.social replied  ·  activity timestamp 4 months ago

Hi @shauna I'm part of such a community at @nf-core@mstdn.science
We build and collect analysis pipeline made with #Nextflow , we have existed since 2018 and have such a community of contributors spread all over the world: https://nf-co.re/contributors
I'd be happy to represent our community 🚀

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