iiinova — where your digital self keeps evolving

Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 02/10/2026

Oh. By the way ... poster and talk were modestly successful, measured in feedback and new users.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 30/09/2026

My first poster since more than 10 years.... #MOPRED symposium Frankfurt, Germany.

Poster showing the Centre for Scientific Computing in Frankfurt, Germany. Or rather it's infrastructure.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 25/09/2026

I made a screencast. This is not the final version. I am merely testing, how it will look on Mastodon. Wondering if it will display well at all. This screencast is a) accelerated, b) shrank, c) incomplete and d) recorded on an "old" cluster. I hope with new […] [Original post on fediscience.org]

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 13/09/2026

Dear Bubble, the far right is on the rise - not just in Germany. But that a Nazi party won an election in a German country state, 80 years after WWII, made the headline in many papers. And it concerns many of you. I have many friends and acquaintances […] [Original post on fediscience.org]

Protest sign, quoting an AfD member who wants to found a new SA to "clean up" society.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 20/08/2026

Today? Among other things: - wrote a looong mail for our new "PR" colleague. She asked wonderful questions about #HPC and the local research landscape. Right to the point. I hope, I helped her. - almost finished my talk about supporting #Snakemake for #HPC […] [Original post on fediscience.org]

Slide with a Don Quichotte sketch of mine and some reasons, why admins should not frown when talks come to workflow management systems.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 29/07/2026

As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement. Next Monday I will start on a new position […] [Original post on fediscience.org]

An optional slide to introduce the pair programming concept. A few lines with bullet points to guide the speaker. Background: A young couple in fancy clothing on a beach with some birds and the moon in the background. Sketch with coal and sanguine.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 01/07/2026

Did a sketch. Again. Always wanted a background image for "now we are doing some pair programming and what is that"-slide. #teaching #programming #pairprogramming

Downsized scan of a charcoal and sanguine sketch on bamboo paper. It shows a young couple on a beach holding hands. They are elegantly dressed. And we see the partial cloud covered moon as well as a couple of birds in the background.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 20/06/2026

... and this is how it will +/- look like in the final slide set. I might extend it, so that it fits better in a 16:9 background. #LaTex #beamer #OpenEducationalResource

Screenshot "Onboarding", the sketch from the earlier post, embedded in a slide, displaying course topics (unfinished, so only a part of all chapters is shown).

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 20/06/2026

Onboarding. Cartoon image for courses. Idea after en.wikipedia.org/wiki/Dropping_the_… Turn's out simple printer paper is good to scan and awful to sketch on. #teaching #sketching

A pilot climbing a ship's staircase (charcoal with oil on simple printer paper)

A pilot climbing a ship's staircase (charcoal with oil on simple printer paper). Slightly enhanced in comic style with GIMP

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 21/04/2026

Ultimately, the plugin has a script on board, to create a mini knowledge graph, illustrating the dependency of input data, configuration, the workflow itself and a published report:

An example knowledge graph referencing 4 nanopublications describing:
- a dataset
- a configuration
- a deposited workflow report
- the workflow itself

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 11/04/2026

Had a wonderful discussion at the #osr26uk about social media, the #fediverse and science communication. I am a firm believer of REAL, venture capital free, social media. Yet, many institutions still refrain from posting to Mastodon. They cannot appreciate […] [Original post on fediscience.org]

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 17/03/2026

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.

2 of 3 continuous integration workflows are working

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 06/03/2026

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 […] [Original post on fediscience.org]

An example (dummy) knowledge graph describing a) a Snakemake workflow b) an example data set and c) an example analysis report for this workflow

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 25/02/2026

Today, I got a book present! Courtesy of @mavieth - Thank you so much! #NFDI #RSE, #RDM #OpenScience

Booklet about current considerations in computational research, data and software management.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 20/02/2026

All in all, the last year has been eventful. Not so much new functionality, but accounting for LOTS of exceptions on various clusters. It is time to move forward at the #SnakemakeHackathon2026 !

lines of code (LOC) development for the Snakemake Executor Plugin for SLURM over time. Displayed are the LOCs for different directories within the repository.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 30/12/2025

My first time ever on this list 😉 . While I don't like gamification, it is certainly something I couldn't miss today when cleaning tabs. #nanopub #gamification

Most active nanopub users this month. My name is last on the list.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 15/12/2025

@wikipathways @egonw Next attempt. Just using these libs: library(rWikiPathways) library(XML) library(dplyr) library(igraph) library(ggraph) library(ggplot2) Still need to polish and work on the colour scale, though. Honestly? I, considering my workload, I […] [Original post on fediscience.org]

overlay plot of a wikipathway showing over- and under expressed genes in red, resp. blue.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 08/12/2025

@tschfflr I compete with my yesterday's deeds. Not as nice, but tasty.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 05/12/2025

@egonw a few days ago, I updated bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package! Today, after quite some tinkering, I managed to overly differential expression results. This is not stable code, yet. The […] [Original post on fediscience.org]

Result of an R-Script illustrating downregulation (shades of blue) in a Drosophila pathway. The dataset was small, the results not reliable, the biological interpretation not feasible.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 26/11/2025

To highlight the accomplishment a screenshot. It shows a Snakemake data analysis workflow running on "my" HPC system. Or rather a tiny fraction of a not-so-demanding workflow. Job submission of single core programs, scripts, threaded programs, MPI-programs […] [Original post on fediscience.org]

Screenshopt (just one part) of a Snakemake Workflow running on an HPC-Cluster. One line, indicating the automated partition selection, is highlighted.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 02/11/2025

Just submitted a talk for FOSDEM (been invited). They asked to attach an icon-image for the talk. So I drew one. The compute racks are difficult to identify as such, but this is as far as my aquarelle skills go. #Snakemake #ReproducibleComputing #HPC

A worker Snake, symbolizing the Snakemake workflow system, carrying a box labelled "SLURM plugin". Grim Face. Dark cloud overhead, labelled "policy".

Subtitle: Reproducible computing on HPC clusters against the odds - the Snakemake SLURM plugin

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 07/10/2025

I fooled myself the other day: Was coding with VSC and "confirmed" a suggestion by the lovely Copilot #AI. Little did I know that, some place else, it was creating a test to check for minutes lasting longer than 59 seconds. (The actual time for 60 seconds […] [Original post on fediscience.org]

screenshot of a unit test code showing the need to test for seconds converted to seconds - actually, this only seems ridiculous. And a test converting a duration of 3600 seconds to 3600 which is ridiculous because the time format would then be 1:00:00.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 01/10/2025

My first contribution to #Bioconda - not much, a rather old software. Took a while ...

screenshot of a GitHub notification showing an icon indicating the merger of a pull request

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 09/09/2025

And apparently, the workflow is running with this new `--slurm-qos` flag.

screenshot of a #Snakemake workflow in action.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 09/09/2025

Today, we will continue with some bits of #Python - no Jupyter: I prefer, if my students can code scripts because we will continue later with some #Snakemake. Just some basics: types, loops, conditionals, strings ... Day 2 of a data analytics course in applied #bioinformatics on #HPC systems. 2/n

Screenshot of a Python script converting degrees Fahrenheit to Celsius - still a version with a hard-coded value.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 08/09/2025

This morning: introduction to the shell, then how to work remotely (SSH, terminal multiplexer, scp, rsync, ...) Day 1 of a data analytics course in applied #bioinformatics on #HPC systems. 1/n

Photo of a projector showing the mkdir command.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 07/09/2025

Framapad as an alternative to Google Docs. The default setting seems to be French, but changing to another language is easy enough. Looks pretty good. framapad.org

Framapad Screenshot - generated without account or login.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 06/09/2025

Just loops, string manipulations and lists. And I can demonstrate a Burrows-Wheeler-Transform! #AcademicChatter #teaching #python

Simple python code to demonstrate a burrows wheeler transform. No optimal implementation! Rather, some dummy code.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 02/09/2025

Soooooo close to finalize a paper ... Alas, the Pareto principle still applies. #academicchatter

Snakemake report - screenshot of a heatmap showing differential expression results for unknown loci. To the right, a splicing isoform analysis.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 01/09/2025

Testing course accounts and realizing that your batch system is down. 😨 #HPC #teaching #academicchatter

Screenshot of a terminal showing non-working SLURM commands.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 26/08/2025

Ok, wir brauchen dringend mehr Wissenschaftskommunikation!

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 15/07/2025

Es tut so verdammt gut, ab und an zu erleben, dass man nicht alleine ist. Die Klimakrise ist jetzt und es nicht egal wie lange wir uns gegen #Ökologie, #KlimaSchutz und eine lebenswerte Welt sperren!

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 10/06/2025

On my way to Hamburg, #ISC25. The place where #HPC folks gather to learn about some new hardware trends. Luckily, I will meet some like minded people, too. Those concerned about #usebility , #teaching , #ReproducibleResearch and so on.

Slightly obstructed view from a 🚆 across the river Rhine. And a blurred castle in the background.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 06/06/2025

#Snakemake in a #Tmux session on our #HPC cluster. It is time to start into the weekend! All I have to do is detach the session and leave.

Screenshot of a terminal showing a progressing Snakemake data analysis workflow. Apparently, analysis jobs are automatically submitted to the cluster, the progress so far: a mere 3 %.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 03/06/2025

Man, this was hard. Alas, the Pareto principle still applies. #academicchatter

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 18/05/2025

@BlumeEvolution Wenn es einmal regnet, bemühen wir uns weiterhin alles Wasser im Schuss zu Tal zu führen. Land auf, Land ab gibt es Drainagesysteme gegen Staunässe. Feuchtwiesen? Ökosysteme, die kaum jemand noch kennt. Änderung in Sicht? Kluges Wassermanagement voraus? Eher nicht.

Entwässerungsgraben überhalb der Schwalm. Nordhessen.

Gerade wurden die letzten Büsche abgesägt. Es gibt keinen Schatten mehr.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 14/05/2025

@mainz_de Es ist natürlich schade, dass Nazis einladen und mit einer scheinbar harmlosen, alltäglichen Fragestellung Werbung für sich machen. Man kann davon ausgehen, dass auch hier wieder Stimmung gegen #Verkehrswende und #Klimaschutz gemacht wird. Ich […] [Original post on fediscience.org]

Informationsveranstaltung der #AFD zum Thema "Tempo 30 - Wie geht es weiter?". Eingeladen auch der OB und die Verkehrsdezernentin der Stadt Mainz.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 14/05/2025

As it seems, using Lego aesthetics is legally doubtful: www.lego.com/en-de/legal/notices-an… How do I know? Well, some here might remember the wonderful image collection of Lego minifigures for research data management […] [Original post on fediscience.org]

Chapter cover for a data analysis course. This image shows some running lego minifigures with a roadrunner in the same aesthetic, carrying a laptop.

LEGO is a trademark of the LEGO Group, which does not sponsor, authorize or endorse this image collection.

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 12/05/2025

Guess, I will have plenty of time tomorrow, for non-#HPC related stuff. 🤷‍♂️

Status message, telling that the file server on an HPC system is not working as expected.

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