#nanopub — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #nanopub, aggregated by home.social.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116443839004108636
Now, folks, this is my first release of a Snakemake reporter plugin!
I am pretty proud of it, but it would have been impossible without the input of @johanneskoester , @tkuhn and - most of all - @fbartusch !
What is it about?
Have you ever read a #bioinformatics paper and thought: "Hugh? How did they get there? This is absolutely not #reproducibleComputing , because I cannot apply it!"
The Snakemake Workflow Management System helps researchers by generating a self-contained HTML report with all bells and whistles (all software metadata, runtime stats and publication-ready figures). And yet, I felt it is time to easy writing the materials & methods section.
Declare a worfklow #nanopub using this template: https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk and get a declaration like this: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
Use this reporter plugin and get all metadata reference in one other nano publication: https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE
1/3
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Aaand, we created a template for a research software management plan by @saranjeet : https://w3id.org/np/RA8YoWqMb6R1HFtFDl3Sr2MlCd8l3ptn-NUGWH4CT398A
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2/3 accomplished ✅
Now, for a release a dependency has to be released with my two fixes, which have already been merged. Then, the world will see a new #nanopub application.
A #SnakemakeHackathon2026 result.
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I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
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I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
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I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
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I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
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I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
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What do you see here? This is an example knowledge graph describing a #Snakemake analysis workflow. You see the workflow description, a linked data set and a linked report.
All work done to boost #HPC user support for those conducting their workflows on HPC systems (you can run Snakemake on other platforms, too).
My to-do list:
- an assertion template for workflows: ✅
- another for reports: ✅ (simple datasets are already in the #nanopub verse)
- a plugin to gather software metadata and publish as a nanopub ❌ (half done: #SnakemakeHackathon2026 )Kudos to @nanopub / @tkuhn and @johanneskoester - without them this pursuit would (have been) futile! And my feeling is that @fbartusch will play an important role in any further development ...
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@Dutch_Reproducibility_Network
In fact, I am a #Snakemake co-maintainer and teacher. I was not aware of WorkflowHub - and that was an omission on my part. We actually support and favour this kind of registration: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#uploading-workflows-to-workflowhub
In my original post, I also neglected to mention the integration of WorkflowHub with #RO-Crate and in turn, the integration of RO-Crates with nanopubs. I am actively working on a better support for #nanopub and RO-Crates with @fbartusch. The question, how I teach that stands: The #HPC world (at least my bubble) is not really supportive for #ReproducibleComputing . All #OpenScience shenanigans are frowned upon. And PIs in my vicinity are still on this level: https://phdcomics.com/comics/archive.php?comicid=1531 - so, how do we educate the educators?
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Just a minute ago, I accidentally discovered Workflowhub (https://about.workflowhub.eu/) when browsing through a few Nanopubs. I was not aware of this repository.
A first thought: "Yet another repository to register #FAIR materials? Seriously?" Then again, I am all in favour of #reproducibleComputing and want to see more of it.
On the other hand: transparency in our work is central to the #OpenScience idea. NOT cluttering a file space so that we can be transparent in our work is paramount.
Lately, we have seen #nanopub, #ROcrates, and apparently WorkflowHub, too. (This is by no means a comprehensive list.) I wonder: Are we getting too many solutions to keep up-to-date? Are we risking frightening young researchers with the high standards we are setting? We are by no means where we want to be in terms of #transparency and #reproducibility in research, or are we?
Note, that I understand how competing systems and tool sets arise. Still, my nonrhetorical questions (1 & 2) stand.
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> Your abstract 'Live Demo: From Snakemake Run to Scholarly Record - Automatic Nanopublications & Workflow Run RO‑Crate Generation' has been successfully submitted. It is registered with the number #150. You will be notified by email with the submission details.
I have quite some work to do ...
PS should have tagged you @fbartusch 😉
#nanopub #ROcrate #Snakemake #derse26 -
Where will I be in early March 2026?
In Stuttgart! At the deRSE conference. I intend to submit a couple of work items dealing with my favourite workflow management system. And the call for contributions is open: https://mastodon.social/@de_rse/115270954346336457
To give you an idea of what I have in mind, a few hashtags:
#Snakemake #nanopub #fairdatamanagement #Fair #ReproducibleComputing
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Oh! Here at the #isc25 I noticed, I got my first #nanopub PR merged: https://github.com/Nanopublication/nanopub-py/pull/193 🥳
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🧐 Everything you can do with #nanopublications in our #RIOJournal on #Pensoft's blog👇
Our #nanopub pilot project with @knowledgepixels gives our authors & readers several opportunities to use #nanopubs to contribute to #published knowledge in a #FAIR manner.
https://blog.pensoft.net/2023/05/17/how-it-works-nanopublications-linked-to-articles-in-rio-journal/
#openscience #openresearch #scholarlypublishing #journals #research #researchers #researchpaper #scientificresearch #scientists #scientificpaper #nanopubs #scholcomm