Daniel Siegle
@danielsiegle.bsky.social
Teaching Biology at NCSSM
Reposted by 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.
Today, building a fence with solar can be cheaper than using wood.
November 10, 2025 at 8:10 AM
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.
Today, building a fence with solar can be cheaper than using wood.
Reposted by Daniel Siegle
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 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
October 26, 2025 at 1:48 PM
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 🧶🧬 🧪
One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪
Reposted by Daniel Siegle
It’s not the thought that counts: Allostasis at the core of brain function
www.cell.com/neuron/fullt...
#neuroscience
www.cell.com/neuron/fullt...
#neuroscience
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 ...
www.cell.com
October 18, 2025 at 1:54 PM
It’s not the thought that counts: Allostasis at the core of brain function
www.cell.com/neuron/fullt...
#neuroscience
www.cell.com/neuron/fullt...
#neuroscience
Reposted by Daniel Siegle
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...
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...
October 16, 2025 at 4:54 PM
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...
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...
Reposted by Daniel Siegle
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...
September 22, 2025 at 9:16 PM
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...
Reposted by Daniel Siegle
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
#Blender #b3d #MolecularNodes #GeometryNodes
September 19, 2025 at 7:28 PM
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
#Blender #b3d #MolecularNodes #GeometryNodes
Reposted by Daniel Siegle
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
TIL that for some people with irreparably damaged corneas, you can pull one of their teeth, drill a hole in it, install an artificial lens, sew it into their cheek (so tissue attaches), then pull it out and stick it in their damaged eye, and ... it works fine!?! www.nbcboston.com/news/health/...
Man, 34, is no longer blind after tooth is implanted in eye in 'crazy' surgery
Tooth-in-eye surgery sounds like science fiction, but it can help people with severely damaged corneas see again. A patient and his doctors describe what it's like.
www.nbcboston.com
September 12, 2025 at 3:04 PM
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
Reposted by Daniel Siegle
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.
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.
Center for the Alignment of AI Alignment Centers
We align the aligners
alignmentalignment.ai
September 11, 2025 at 1:17 PM
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.
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.
Reposted by Daniel Siegle
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.
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.
September 3, 2025 at 9:09 PM
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.
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.
Reposted by Daniel Siegle
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.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
August 20, 2025 at 10:42 AM
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.
Another company invented a chatbot that can talk like us and we reorganised the entire tech industry around it.
Reposted by Daniel Siegle
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...
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...
August 13, 2025 at 5:38 PM
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...
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...
Reposted by Daniel Siegle
A thread of protein-themed card, board, and video games 🧵
Play the PDB board game that explores the process of structure discovery and deposition. Then, move on to the next project...but keep an eye on the competition and try not to get scooped! #GenCon
pdb101.rcsb.org/lear...
pdb101.rcsb.org/lear...
PDB101: Learn: Other Resources: PDB50 the Game
A PDB “worker placement” board game that explores the process of structure discovery
pdb101.rcsb.org
August 4, 2025 at 8:07 PM
A thread of protein-themed card, board, and video games 🧵
Reposted by Daniel Siegle
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+)
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
Play the PDB board game that explores the process of structure discovery and deposition. Then, move on to the next project...but keep an eye on the competition and try not to get scooped! #GenCon
pdb101.rcsb.org/lear...
pdb101.rcsb.org/lear...
PDB101: Learn: Other Resources: PDB50 the Game
A PDB “worker placement” board game that explores the process of structure discovery
pdb101.rcsb.org
August 2, 2025 at 6:16 PM
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+)
You can download a PDF, and print out the parts, or play online ⬇️ (Age 10+)
Reposted by Daniel Siegle
We turned medicinal chemistry into a card game, which takes 3-10 years to play.
PDF: jabde.com/wp-content/u...
PDF: jabde.com/wp-content/u...
July 25, 2025 at 8:45 AM
We turned medicinal chemistry into a card game, which takes 3-10 years to play.
PDF: jabde.com/wp-content/u...
PDF: jabde.com/wp-content/u...
Reposted by Daniel Siegle
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...
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.
elevanth.org
July 9, 2025 at 1:40 PM
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...
Reposted by Daniel Siegle
🤖 Apropos of , 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...
huggingface.co/spaces/meg/w...
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.
huggingface.co
July 11, 2025 at 4:20 PM
🤖 Apropos of , 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...
huggingface.co/spaces/meg/w...
Reposted by Daniel Siegle
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...
Barba, Lorena A. (2025). Embracing GenAI in Engineering Education: Lessons from the Trenches. figshare. Presentation. doi.org/10.6084/m9.f...
Embracing GenAI in Engineering Education: Lessons from the Trenches
Talk at the SciPy Conference, July 9, 2025. Tacoma, Washington.This talk presents a candid reflection on integrating generative AI into an Engineering Computations course, revealing unexpected challen...
doi.org
July 10, 2025 at 1:37 PM
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...
Barba, Lorena A. (2025). Embracing GenAI in Engineering Education: Lessons from the Trenches. figshare. Presentation. doi.org/10.6084/m9.f...
Reposted by Daniel Siegle
1/4
🚀 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
🚀 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
July 8, 2025 at 4:26 PM
1/4
🚀 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
🚀 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
Reposted by Daniel Siegle
This lab cranks out the tastiest-sounding protein design methods and I'm here for it
Presenting RISoTTo, a molecular context-aware model for RNA sequence design, building on our work with PeSTo (for protein binding interface prediction) and CARBonAra (for protein design).
📄 Preprint: www.biorxiv.org/content/10.1...
💻 Code & more coming soon!
#RNAdesign #RNAbiology #AI4Science
📄 Preprint: www.biorxiv.org/content/10.1...
💻 Code & more coming soon!
#RNAdesign #RNAbiology #AI4Science
www.biorxiv.org
June 22, 2025 at 12:26 PM
This lab cranks out the tastiest-sounding protein design methods and I'm here for it
Reposted by Daniel Siegle
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/
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…
rosettacommons.org
June 6, 2025 at 8:34 PM
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/
Reposted by Daniel Siegle
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...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 29, 2025 at 9:50 AM
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...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Reposted by Daniel Siegle
Youtube link is live: youtu.be/wTzRQynRBs0?...
February 11, 2025 at 12:33 PM
Youtube link is live: youtu.be/wTzRQynRBs0?...
Reposted by Daniel Siegle
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
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.
github.com
January 23, 2025 at 2:12 PM
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
Reposted by Daniel Siegle
searching for pdb entries and google randomly did this
January 23, 2025 at 7:25 PM
searching for pdb entries and google randomly did this