Daniel Siegle

A thread of protein-themed card, board, and video games 🧵

A new one to me: a protein structure board game.

You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)

We turned medicinal chemistry into a card game, which takes 3-10 years to play.

PDF: jabde.com/wp-content/u...

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

Durham’s Once City Center struck by lightning at 2:33 pm (via a friend)

Durham’s One City Center building struck by lightning at 2:33 pm (via a friend) #ncwx

Watermark Demo - a Hugging Face Space by meg Add a watermark to any video file by uploading both the video and the watermark image. The result is a watermarked video.

🤖 Apropos of <gestures at world>, reminder that AI-generated videos can--and ought to--minimally have visible watermarks disclosing that they are synthetic. You can do it trivially using @hf.co tools. Before sharing something synthetic, please run it through this.
huggingface.co/spaces/meg/w...

Presentation slides for my talk yesterday at #SciPy2025

Barba, Lorena A. (2025). Embracing GenAI in Engineering Education: Lessons from the Trenches. figshare. Presentation. doi.org/10.6084/m9.f...

Thank you! I shared your preprint with colleagues this spring and was eagerly awaiting the lessons learned from last semester.

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🚀 Announcing the 2025 Protein Engineering Tournament.

This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️

#AIforBiology #ClimateTech #ProteinEngineering #OpenScience

This lab cranks out the tastiest-sounding protein design methods and I'm here for it

1-day Protein Design AI-Driven Design of Biologics: Hands-on Guide to Using State-of-the-Art ML Protein Models brought to you by the Rosetta Commons Summer RosettaCon 2025 Workshop. Applications are now open, apply her…

Consider joining us for the SRC2025's 1-day Protein Design: One-day novice-level course surveying popular tools and workflows for modern protein design with brief exploration of common applications including antibody design and binder design. rosettacommons.org/2025/06/03/1-day-protein-design/

Google Colab

Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...

Youtube link is live: youtu.be/wTzRQynRBs0?...

GitHub - PatWalters/resources_2025: Machine Learning in Drug Discovery Resources 2024 Machine Learning in Drug Discovery Resources 2024. Contribute to PatWalters/resources_2025 development by creating an account on GitHub.

Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...

searching for pdb entries and google randomly did this

New book "Explanation in Biology" with Cambridge University Press is out & open access!

Covers (1) causal explanation & (2) non-causal/mathematical explanation in life sciences--bio, neuro, etc 🌿🧬🧠

Introduction to philosophical work on scientific explanation!

www.cambridge.org/core/element...

YouTube video by Felix Petersen Convolutional Differentiable Logic Gate Networks - NeurIPS Oral - difflogic

If you're excited about #AI with #logic, check out our fully animated video on YouTube: youtu.be/FKQfMwFZvIE