If I could go back in time with this manuscript, I would have either designed the workflow to process the ~6000 possibly useful datasets in batches of 100 or so, or done the filtering to the actual useful ~700 of ~6000 in one part of the workflow, and then the analysis of the useful ones in another part of the workflow.

I didn't imagine that there would be fifteen odd processing and analysis steps on the ~6000 files -> ~91,000 targets in the workflow. 🤦‍♂️

#RStats #Bioinformatics #Academia

If I could go back in time with this manuscript, I would have either designed the workflow to process the ~6000 possibly useful datasets in batches of 100 or so, or done the filtering to the actual useful ~700 of ~6000 in one part of the workflow, and then the analysis of the useful ones in another part of the workflow.

I didn't imagine that there would be fifteen odd processing and analysis steps on the ~6000 files -> ~91,000 targets in the workflow. 🤦‍♂️

#RStats #Bioinformatics #Academia

Does anyone know if the code for generating all of the underlying bits for #recount3 (genome indices, exons, genes, etc) for a different genome organism (i.e. zebrafish) is available publicly?

I know of the monorail-external repo that helps someone running their own human or mouse samples in the same workflow, but I've got data from zebrafish that I'd love to run similarly.

#Bioinformatics #Bioconductor #RStats

Maybe @benlangmead (or another) knows of something I missed?

Does anyone know if the code for generating all of the underlying bits for #recount3 (genome indices, exons, genes, etc) for a different genome organism (i.e. zebrafish) is available publicly?

I know of the monorail-external repo that helps someone running their own human or mouse samples in the same workflow, but I've got data from zebrafish that I'd love to run similarly.

#Bioinformatics #Bioconductor #RStats

Maybe @benlangmead (or another) knows of something I missed?

🔬 Excited about structure-based drug design?
Join us at the 38th Molecular Modelling Workshop in Erlangen (10.03.2026) and get hands-on with ProteinsPlus!
🧬 For more information see: https://www.denbi.de/training-courses-2026/2023-proteinsplus-supporting-structure-based-design-on-the-web-38th-molecular-modelling-workshop-2026
#MolecularModelling #Bioinformatics #ProteinsPlus #DrugDesign

🔬 Excited about structure-based drug design?
Join us at the 38th Molecular Modelling Workshop in Erlangen (10.03.2026) and get hands-on with ProteinsPlus!
🧬 For more information see: https://www.denbi.de/training-courses-2026/2023-proteinsplus-supporting-structure-based-design-on-the-web-38th-molecular-modelling-workshop-2026
#MolecularModelling #Bioinformatics #ProteinsPlus #DrugDesign

50% of #bioinformatics is just joins on poorly constructed primary keys..

select * from 'log_tpm.csv' exp join 'b_mapping.csv' bm on bm.b_number = exp.column000 join 'dh10b_2.csv' dh on dh.gene_name = bm.gene_name limit 1

50% of #bioinformatics is just joins on poorly constructed primary keys..

select * from 'log_tpm.csv' exp join 'b_mapping.csv' bm on bm.b_number = exp.column000 join 'dh10b_2.csv' dh on dh.gene_name = bm.gene_name limit 1

Hi lazywell,

is there a standard CLI tool that can be used to extract all the descendants (rdf:subClass ? ) of a given term from a local OWL ontology file ?

I wrote a stupid java xml tool but I'd like a tool that understands the OWL spec (I don't)

#rdf #ontology #owl #bioinformatics

“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