| Personal website | https://jeandelmotte.com/ |
New blog post: I got tired of having repetitive arguments explaining why I think it’s OK to be skeptical of LLMs for coding, so I wrote six and a half thousand words on the topic that I will be referring people to from now on.
Importance of taking Single Amino Acid Variant and accessory proteome variability into account in Data Independent Acquisition Proteomics: illustrated with Legionella pneumophila analysis https://www.biorxiv.org/content/10.64898/2026.04.01.715759v1.full.pdf+html
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#proteomics #prot-preprint
Cet article explique l’apport de l’installation du modèle de transcription d’audio en texte Whisper sur un ordinateur personnel, puis décrit trois méthodes d’installation et d’utilisation de ce modèle d’intelligence artificielle en local qui évitent de passer par des logiciels tiers. Les personnes qui visent une utilisation immédiatement efficace peuvent directement installer la bibliothèque Python « … Continuer la lecture de « Transcription de fichiers audio : installer et utiliser Whisper en local »
me: I should add some interactivity to my plots
also me: *Shoves fully playable DOOM into an SVG file*
cargo build --features cli,doom
kuva doom -o doom.svg
open in browser. that's it.
Yes, it's April 1st, but this is real 😅
https://psy-fer.github.io/kuva/doom.html
📢 2 ressources "geeks" de la Forge* !
addr : apprendre les adresses réseau
https://addr.forge.apps.education.fr/
rwx : apprendre les permissions Linux
https://rwx.forge.apps.education.fr/
Parmi les 431 de notre nouvelle Ressourcerie
https://ressourcerie.forge.apps.education.fr/
Elle même sélection des 8845 dépôts de notre Atelier (GitLab)
https://forge.apps.education.fr/explore/
*Écosystème collaboratif de création et de partage de ressources éducatives libres géré et animé par la communauté enseignante et soutenu par l'Éducation nationale (fr).
Accurate genome annotation remains challenging as assembly quality often exceeds annotation reliability. Resolving ambiguities of gene presence, absence, and orthology typically requires integrating two complementary lines of evidence: sequence homology between species and the conservation of gene order (i.e., synteny). BLAST remains the standard for homology detection, yet its raw output can be difficult to interpret. Existing tools address this challenge but operate at opposing scales. Alignment viewers provide detailed pairwise statistics without genomic context, while synteny tools offer chromosome-scale perspectives without sequence-level resolution. To fill this intermediate gap, we developed Novabrowse, an interactive BLAST results interpretation framework featuring high-resolution multi-species synteny analysis, chromosomal rearrangement investigation, ortholog detection, and gene signal discovery. Users define a genomic region of interest in a query species and/or use custom sequences, then select one or more subject species for comparison. The pipeline retrieves query gene sequences via NCBI API integration and performs BLAST searches against each subject transcriptome or genome. Results are presented via an interactive HTML file featuring alignment statistics, chromosomal maps, coverage visualizations, ribbon plots, and distance-based clustering of high-scoring segment pairs into putative gene units. We demonstrate these capabilities by investigating Foxp3, Aire, and Rbl1, three highly conserved vertebrate genes, in the recently assembled genome of the newt Pleurodeles waltl. Foxp3 and Aire have not been described in any salamander species to date, despite availability of multiple assemblies and extensive transcriptomic datasets. Using Novabrowse, we discovered conserved loci and gene signals for both genes in P. waltl, the presence of which was subsequently confirmed via Nanopore long-read RNA sequencing. In contrast, Rbl1 analysis uncovered a chromosomal rearrangement at its expected locus with no gene signal detected, indicating a gene loss specific to P. waltl despite the gene's retention in the closely related axolotl (Ambystoma mexicanum). Our findings demonstrate Novabrowse's capacity for evidence-based evaluation of annotation artifacts, an essential capability as high-quality assemblies become more available for phylogenetically diverse species. Novabrowse is open source (MIT license) and freely available at:https://github.com/RegenImm-Lab/Novabrowse. ### Competing Interest Statement The authors have declared no competing interest. Knut and Alice Wallenberg Foundation, https://ror.org/004hzzk67 Cancerfonden, 23 3047 Pj Crafoord Foundation, https://ror.org/02hwwbr17, #20230825
James Bennett
European Physical Society(EPS)
Stephen Heard
Codeberg Status
PastelBio
Clem 🌍🌻⏚
James Ferguson 
Le Libre Éducatif
bioRxiv Genomics
Christian Meesters