Daniel Siegle

Solar’s price drop is astonishing: panels are now 98% cheaper than when I first analyzed them in 2004.

Today, building a fence with solar can be cheaper than using wood.

A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩‍🔬👩‍🎓 in just a few weeks!

One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪

It’s not the thought that counts: Allostasis at the core of brain function The authors review evidence that the primary function of the brain, supported by distributed neural systems, is the predictive regulation of physiology (i.e., allostasis). An example from Alzheimer’s ...

It’s not the thought that counts: Allostasis at the core of brain function
www.cell.com/neuron/fullt...
#neuroscience

I decided to experiment with my own (small) protein design competition!

It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.

You submit a modal script, I run it and test on benchbb.bio

blog.booleanbiotech.com/vhh-competit...

Good thing it's on that hill

If only we had some way of know what things were really true. Some system of testing over time, where we could build up our knowledge about the best way to do things...

Hello! I'm Behnoush, structural biology scientist from the Broad Institute. I also like to combine proteins structures and other scientific topics with art. Here are some journal cover arts I've created recently. Hope to find old and new friends here.
#Blender #b3d #MolecularNodes #GeometryNodes

This is the shit they’re defunding. Scientists can make your teeth see so you can get back to balling and they want to take that away from you forever

Center for the Alignment of AI Alignment Centers We align the aligners

Q. Who aligns the aligners?
A. alignmentalignment.ai

Today I’m humbled to announce an epoch-defining event: the launch of the 𝗖𝗲𝗻𝘁𝗲𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗼𝗳 𝗔𝗜 𝗔𝗹𝗶𝗴𝗻𝗺𝗲𝗻𝘁 𝗖𝗲𝗻𝘁𝗲𝗿𝘀.

What are your pros/cons of using AI in science?

Feel free to respond wrt use or harm in the design of experiments, coding experiments, coding analysis, brain storming analysis, summarizing literature, synthesis of ideas, modeling, novel model development, mathematical proofs, writing, editing.

It says a lot about society that the reaction to AlphaFold was a couple of excited news articles and a tiny amount of funding.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.

Why PETase for our tournament? In 2024, the world made about 30 million tonnes of PET plastic, most from fossil fuels.

PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.

Register by Oct 17 alignbio.org/protein-engi...

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