“Analysis of Biological Data with Python” started today for our biology bachelor students 🧬🐍

If you are interested in learning Python for data analysis, the course slides are freely available here:
https://github.com/bpucker/teaching/tree/master/WBIO-A-07

#Python #DataAnalysis #Biology #OpenEducation #OpenScience #Teaching #Bioinformatics #BigData #DataScience
@PuckerLab

“Analysis of Biological Data with Python” started today for our biology bachelor students 🧬🐍

If you are interested in learning Python for data analysis, the course slides are freely available here:
https://github.com/bpucker/teaching/tree/master/WBIO-A-07

#Python #DataAnalysis #Biology #OpenEducation #OpenScience #Teaching #Bioinformatics #BigData #DataScience
@PuckerLab

A 2026 look at three bio-ML opinions I had in 2024

https://www.owlposting.com/p/a-2026-look-at-three-bio-ml-opinions

#HackerNews #bioML #bioinformatics #future2026 #opinions #technology #trends

January 2026 WikiPathways update: 134 edits by 3 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/213 Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

January 2026 WikiPathways update: 134 edits by 3 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/213 Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

@jerven okay, rough estimate of the number of owl:sameAs links now in the @wikipathways RDF (part of the release on the 10th):

- 1250+ owl:sameAs to SwissLipids
- 5000+ owl:sameAs to @lipidmaps.bsky.social
- 1600+ owl:sameAs to @rhea-db.bsky.social
- 77k+ owl:sameAs to UniProtKB

(powered by @wikidata via their SPARQL)

#bioinformatics #sparql #cheminformatics

@jerven okay, rough estimate of the number of owl:sameAs links now in the @wikipathways RDF (part of the release on the 10th):

- 1250+ owl:sameAs to SwissLipids
- 5000+ owl:sameAs to @lipidmaps.bsky.social
- 1600+ owl:sameAs to @rhea-db.bsky.social
- 77k+ owl:sameAs to UniProtKB

(powered by @wikidata via their SPARQL)

#bioinformatics #sparql #cheminformatics

new blog post: "PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge" https://chem-bla-ics.linkedchemistry.info/2026/01/05/plantmetwiki.html https://doi.org/10.59350/wyz5v-vts33

"I am happy that Elena and Denise pulled me into a collaboration to create an RDF-based knowledge graph about plant pathways."

tl;dr: https://plantmetwiki.bioinformatics.nl/

Replying to this post makes it show up in my blog.

#plants #bioinformatics #openscience

new blog post: "PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge" https://chem-bla-ics.linkedchemistry.info/2026/01/05/plantmetwiki.html https://doi.org/10.59350/wyz5v-vts33

"I am happy that Elena and Denise pulled me into a collaboration to create an RDF-based knowledge graph about plant pathways."

tl;dr: https://plantmetwiki.bioinformatics.nl/

Replying to this post makes it show up in my blog.

#plants #bioinformatics #openscience

Working with biological sequences… in the terminal 🔥

🧪 **SeqTUI** — A terminal-based sequence data viewer & toolkit.

🧬 View, translate, convert to FASTA, extract SNPs & combine huge alignments.

🦀 Written in Rust & built with @ratatui_rs

⭐ GitHub: https://github.com/ranwez-search/SeqTUI

#rustlang #ratatui #tui #bioinformatics #terminal #cli #opensource

Working with biological sequences… in the terminal 🔥

🧪 **SeqTUI** — A terminal-based sequence data viewer & toolkit.

🧬 View, translate, convert to FASTA, extract SNPs & combine huge alignments.

🦀 Written in Rust & built with @ratatui_rs

⭐ GitHub: https://github.com/ranwez-search/SeqTUI

#rustlang #ratatui #tui #bioinformatics #terminal #cli #opensource

Anyone know what software is used to generate these amino acid sequence alignments figures?
#bioinformatics

Anyone know what software is used to generate these amino acid sequence alignments figures?
#bioinformatics

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

Playing with XML+XSLT=SVG because I just hate circos.

#bioinformatics #svg #xml #xslt

“Complex end-to-end tests using #Guix G-expressions” (Sept. 2025)
https://systemreboot.net/post/complex-end-to-end-tests-using-guix-g-expressions.html

Nice post by Arun Isaac showing how to put G-expressions to good use to compose a complex pipeline, in this case illustrated with #bioinformatics.

new blog: "WikiPathways curation reports on profile pages" https://doi.org/10.59350/s7vw2-r7y02 https://chem-bla-ics.linkedchemistry.info/2025/11/30/wikipathways-curation-reports-on-profile-pages.html

Replies to this post show up as comments in the blog post.

#bioinformatics #cheminformatics #curation

@wikipathways still has a good number (200 to 250) pathways that do not have a single reference (which does not mean no references were used): https://www.wikipathways.org/wikipathways-collection/index2#at-least-one-reference

I think we need some gamification here... a few tools that take the GPML or RDF and suggest a relevant lit reference, which then gets posted to this issue tracker (https://github.com/wikipathways/pathway-curation-tasks/issues), listing the WPID and PMID, PMCID, or DOI, and ideally the graphID of the DataNode or Interaction

#bioinformatics #gamification #biocuration