iiinova — where your digital self keeps evolving

Brian Naughton @btnaughton.bsky.social · 28/06/2026

new blogpost: Nasal sprays and peptides for virus protection blog.booleanbiotech.com/nasal-sprays...

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Brian Naughton @btnaughton.bsky.social · 11/03/2026

I wrote a primer on AI antibody design, published on Asimov press. www.asimov.press/p/antibody-d...

asimov.press

How to Design Antibodies

A step-by-step guide to making de novo binders.

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Brian Naughton @btnaughton.bsky.social · 09/02/2026

Excellent, comprehensive rundown of the state of bio lab automation by @owlposting1.bsky.social In retrospect, it's an important topic that has had almost zero discussion over the years! A fun surprise to see some decade-old(!) work show up in there too. www.owlposting.com/p/heuristics...

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Brian Naughton @btnaughton.bsky.social · 19/01/2026

github.com/adaptyvbio/p... Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv. Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art! I'm happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...

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Brian Naughton @btnaughton.bsky.social · 19/01/2026

Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv. Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art! I'm also happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...

x.com

Tudor-Stefan Cotet (@CotetTudor) / X

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Brian Naughton @btnaughton.bsky.social · 04/01/2026

Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...

blog.booleanbiotech.com

Boolean Biotech

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Brian Naughton @btnaughton.bsky.social · 30/12/2025

Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser. hgbrian.github.io/alignism/ - The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!

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Brian Naughton @btnaughton.bsky.social · 26/12/2025

I semi-vibe coded a frontend for all the protein folding tools I've been running. It runs on modal and has 5 different open-source algorithms: Chai1, Boltz2, AF2, Protenix(-mini). Not 100% polished but hopefully of use to some use to people in the field! github.com/hgbrian/fold...

github.com

GitHub - hgbrian/foldism: protein folding app running on modal

protein folding app running on modal. Contribute to hgbrian/foldism development by creating an account on GitHub.

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Brian Naughton @btnaughton.bsky.social · 13/12/2025

I wrote up a short blogpost on using Claude Code / Opus 4.5 for computational biology blog.booleanbiotech.com/claude-code-...

blog.booleanbiotech.com

Boolean Biotech

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Brian Naughton @btnaughton.bsky.social · 30/10/2025

A treasure trove of biotech and early SV oral histories by Sally Hughes: digicoll.lib.berkeley.edu/search?p=%28... Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.

digicoll.lib.berkeley.edu

( (creator:[Hughes, Sally Smith])) - Search Results - Digital Collections

Digital Collections Search Results.

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Brian Naughton @btnaughton.bsky.social · 27/10/2025

I’ve been testing BoltzGen a bit recently and while I haven’t done any experimental testing yet, the quality of the software is very clear. It installs, runs, logs everything, has tons of options. Very excited to test out the designs irl!

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Brian Naughton @btnaughton.bsky.social · 16/10/2025

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...

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Brian Naughton @btnaughton.bsky.social · 29/09/2025

Another promising VHH model just dropped today from Manifold Bio. This one builds on BindCraft and ColabDesign. MIT license! www.biorxiv.org/content/10.1... The success rates appear to be lower than other tools, but this is highly target-dependent.

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Brian Naughton @btnaughton.bsky.social · 28/09/2025

New blogpost on the latest in AI antibody design. Including some code to easily run Germinal and IgGM on modal! blog.booleanbiotech.com/ai-antibody-...

blog.booleanbiotech.com

Boolean Biotech

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Brian Naughton @btnaughton.bsky.social · 25/09/2025

It has been interesting to use gitingest to paste entire codebases for new tools into Gemini and ask for severe bugs (logic, incorrect variables...). I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...

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Reposted by Brian Naughton

Arc Institute @arcinstitute.org · 24/09/2025

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design. Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

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Brian Naughton @btnaughton.bsky.social · 19/09/2025

A REALLY nice use of nanobanana (Gemini) is cleaning up blurry old images. Of course it depends what you ask for, but it is amazing at keeping the text and content the same.

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Brian Naughton @btnaughton.bsky.social · 13/09/2025

We decided to try to 3d print custom chess pieces. The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work! Left is the gemini image and right is the mesh.

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Brian Naughton @btnaughton.bsky.social · 06/09/2025

I was reminded about Blackett's War by a mention on the @patio11 podcast. Terrific book about operations research / probability theory applied to real world problems. Lots of anecdotes like this...

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Brian Naughton @btnaughton.bsky.social · 13/08/2025

Ibex from Prescient Design arxiv.org/abs/2507.09054 github.com/prescient-de... - antibody folding with performance like Boltz/Chai but up to 100X faster - does not fold the complex, just the antibody - predicts holo and apo forms - sadly, model weights are not freely available

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Reposted by Brian Naughton

Max Fürst @maxfus.bsky.social · 01/08/2025

Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago. fuerstlab.shinyapps.io/SeqNovelty/ quick 🧵

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Brian Naughton @btnaughton.bsky.social · 25/07/2025

After many months heads down, we at Decade are growing! We are hiring a protein biochemist to help us radically improve cancer treatment. If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers

decade.bio

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Brian Naughton @btnaughton.bsky.social · 19/07/2025

Asking Claude to research binder designs metrics and it gave me my own blogpost back! Time to start writing for the AIs? marginalrevolution.com/marginalrevo...

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Brian Naughton @btnaughton.bsky.social · 23/06/2025

Vibe coded a run progress simulator with Gemini Canvas. It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs. Still very impressive! hgbrian.github.io/run_progress...

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Brian Naughton @btnaughton.bsky.social · 30/05/2025

I spent way too long on this but I made a small benchmark for OCR of biological sequences. It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works! github.com/hgbrian/bio_...

github.com

GitHub - hgbrian/bio_ocr_minibenchmark: a small OCR benchmark for biological sequences

a small OCR benchmark for biological sequences. Contribute to hgbrian/bio_ocr_minibenchmark development by creating an account on GitHub.

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Brian Naughton @btnaughton.bsky.social · 30/05/2025

BindEnergyCraft claims to improve BindCraft performance using an energy-based objective. "Code will be released soon."

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Brian Naughton @btnaughton.bsky.social · 28/05/2025

Clever mosquito detector, draws a circle around the mosquito so you can squash it. $200 bzigo.com

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Brian Naughton @btnaughton.bsky.social · 21/05/2025

I have been copying some amino acid sequences out of PDFs and so far nothing (Gemini, Claude, ChatGPT) works at >99% accuracy. I have to manually inspect everything! Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?

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Brian Naughton @btnaughton.bsky.social · 05/05/2025

new blogpost: AI and protein patents blog.booleanbiotech.com/ai-protein-p...

blog.booleanbiotech.com

Boolean Biotech

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Brian Naughton @btnaughton.bsky.social · 02/05/2025

We have gotten some really good responses to science questions from platform.futurehouse.org already. Both from "Crow" (short answers) and "Falcon" (deep research). It looks like this is state of the art right now!

platform.futurehouse.org

FutureHouse Platform

AI Agents for Scientific Discovery

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Brian Naughton @btnaughton.bsky.social · 29/04/2025

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...

biorxiv.org

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Brian Naughton @btnaughton.bsky.social · 24/04/2025

There are now a trio of great pieces covering the rapid rise of Chinese biotech: - atelfo.github.io/2024/12/20/w... - centuryofbio.com/p/commoditiz... - www.asimov.press/p/china-trials

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Reposted by Brian Naughton

Alex Crits-Christoph @acritschristoph.bsky.social · 23/04/2025

Results are honestly fascinating and amusing. 1. It succeeded on my first test to identify the function of a protein sequence - it correctly ran BLAST and identified the function although got specific details wrong. It then hallucinated *wildly* about details (domains, active sites) 1/n

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Brian Naughton @btnaughton.bsky.social · 23/04/2025

sciencemachine.ai looks really interesting (default example analysis below) I am not sure how uploading to the browser can work for real sequencing data though. Maybe they will take a bucket url or something.

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Brian Naughton @btnaughton.bsky.social · 22/04/2025

I did not know @plasmidsaurus.bsky.social is doing eukaryote nanopore sequencing now. The price is good, especially $50 extra for extraction. Unfortunately you cannot yet send any tissue, only certain blood and cell culture.

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Brian Naughton @btnaughton.bsky.social · 10/04/2025

Since BoltzDesign1 just got published, people might also be interested in github.com/escalante-bi... by @nboyd.bsky.social It has a nicely flexible system for including custom losses. It's also surprisingly little code on top of Boltz (and the Jaxified Joltz).

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Reposted by Brian Naughton

Babak Alipanahi @babaka.bsky.social · 01/04/2025

Super excited to share that our paper on a multi-modal cell-free RNA foundation model is out! A fantastic collaboration with @genophoria.bsky.social, @fhormozd.bsky.social and the @exai.bio team!

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Brian Naughton @btnaughton.bsky.social · 31/03/2025

Checking into options for home lab testing. A lot of places are now offering the Tasso device or similar for home collection: - mylabsdirect.com/product/comp... - rythmhealth.com - siphoxhealth.com - www.functionhealth.com - www.walkinlab.com

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