Diego Javier Zea

Scientific Modeling Cheatsheet: SciML has published a quick reference cheatsheet translating hundreds of functions between Julia, Python and MATLAB. Click here for more. sciml.github.io/Scientific_M...
#JuliaLang #SciML #Python #MATLAB #ScientificComputing #DataScience #Cheatsheet #Engineering

Julia v1.12.1 is out! 🎈🙃

#JuliaLang

#JuliaLang #Bioinformatics

GitHub - diegozea/MIToS.jl: A Julia package to analyze protein sequences, structures, and evolutionary information A Julia package to analyze protein sequences, structures, and evolutionary information - diegozea/MIToS.jl

🛡️ Confidence boost: refreshed benchmarks and tests now cover 96%+ of the code. Repo: github.com/diegozea/MIT...

🎨 Better structure viz: edit B-factors so you can color atoms/residues by any variable when plotting (e.g., quality, flexibility, or scores).

🗂️ Combining datasets is simpler: merge MSAs by matching sequence names automatically when pairings aren’t specified.

📈 MSA stats at a glance: estimate the effective number of sequences (down-weight redundancy) and quantify the share of “positive” residue pairs under your chosen matrix.

📊 Alignment quality: get the classic sum-of-pairs score for an MSA using a residue substitution matrix (BLOSUM62 by default), with consistent handling of gaps and unknowns.

🧬 Substitution matrices are now first-class: use built-ins like BLOSUM62 or bring your own from BioJulia’s BioAlignments.

Dragon showing the Julia colors and the text: MIToS.jl v3.2

🚀 MIToS.jl v3.2.0 brings cleaner substitution matrices, better MSA quality measures, easier MSA merges, and sturdier PDB handling — plus higher test coverage. 🧵

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

📢 Deadline Extended!
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇

ANR SPPICES Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals

Join the MAGI team at @i2bcparissaclay.bsky.social as part of the ANR SPPICES project 🌶️
This position involves collaboration with members of the ML4NGP network on machine learning & non-globular proteins
Learn more 👉 sppices.notion.site

🚨 We're hiring a Bioinformatics Engineer!
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...

ANR SPPICES Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals

Learn more about the SPPICES project (Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals) here:
sppices.notion.site

Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀

📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

Book/Course

BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !!

@msftresearch.bsky.social

I have the same question. I haven't checked yet.

Yes, before, it was pretty cumbersome and slow. Now, it is the opposite experience 🙂

Screen capture of Google Colab showing their native version of Julia (1.10.8)

@googlecolab.bsky.social now has native support for #JuliaLang! 🎉 No special setup is needed anymore—start coding and sharing your @julialang.org projects! 🚀

Since you knew it, could it have helped more unconsciously, being there feeding the intuitions? 🤔

I am not sure that the Julia's Fibonacci implementation is optimal. Using Val is nice to showcase dispatch, but it hits compilation for every number, and it makes the code type unstable. Conversely, using Val should make the compiler memoize the result for each number. github.com/bddicken/lan...

🚨 I am super happy to announce that our analysis of how the structure of protein-RNA interfaces evolves is now published (early access) at @plos.bsky.social Computational Biology:
doi.org/10.1371/jour...
🧬🧶

Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

Could you add me to the pack if structural bioinformatics and molecular evolution are welcome?

Thanks :)

Hi! I nominate myself :)

Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack!

go.bsky.app/Hv4RKzM

What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊