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I’m relocating this blog to Substack: https://zachocean.substack.com/ Why? I want to make it easier for folks to subscribe via email, I like the Substack post editor, I want more discoverability, and I like how Substack handles embeds of tweets and other substack posts. Let’s see how it goes.
What makes Forever Chemicals forever? - Bryan Johnson Steady Progress and Self-Reflection: 2025 Annual Letter - Permanent Equity The emerging epicenter: Asia’s role in biopharma’s future - McKinsey Is Biopharma Doing Enough to Advance Novel Targets? - L.E.K. Consulting (via Jacob Kimmel’s Creating Therapeutic Abundance) moPPIt: De Novo Generation of Motif-Specific Peptide Binders…
Protein Dojo is a platform for learning protein design by practicing with realistic drug targets and modern computational molecular design tools. I built it over the last few weeks of winter holidays, during family nap times and around holiday celebrations. My goals for this project are twofold. One, I wanted to make somethign useful for people who are just getting into computational molecule…
Chinese Peptides in Silicon Valley - NYTimes PeptiVerse: Peptide Property Prediction - Hugging Face The MPTP Story - J William Langston (MPTP and Parkinson’s) A Multimodal Sleep Foundation Model for Disease Predictions - Nature Medicine (code) NewLimit Update - Jacob Kimmel Creating Therapeutic Abundance - Jacob Kimmel Topos Bio - AI drug discovery for intrinsically disordered proteins…
Not For Human Consumption - Vectorculture Ph.D.s Can’t Find Work as Boston’s Biotech Engine Sputters - WSJ Alignism - Sequence Alignment - hgbrian The Generative Geometric Turn in AI Drug Discovery - LiteFold A Visual Guide to Keytruda - Liam Bai Rebuild Biotech for the AI Era - Benchling
2025 LLM Year in Review - Karpathy Chemical Hygiene - Karpathy A Comprehensive Introduction to AI for Proteins - Tamarind Bio https://x.com/shelbynewsad/status/2003508957155844390 AI drug designer Insilico Medicine aims to generate $300M in Hong Kong IPO - FierceBiotech The Virtual Cell Will Be More Like GWAS Than AlphaFold - Andrew Carroll The ML drug discovery startup trying really, really hard…
Aaron blotnick’s jpm week list: JPM Week 2025 Event List Using Claude Code for computational biology De novo design of luciferases using deep learning Latent X2 Technical Report Immune repertoire profiling for disease pathobiology China’s Biotech Is Cheaper and Faster ChinaRxiv Science Corporation working on organ preservation: A Brain-Computer Interface Company Is Getting Into Organ…
Sugars, ‘Gum,’ Stardust Found in NASA’s Asteroid Bennu Samples AI in biotech investor tweet thread: Jeffrey Low MD on X High throughput binder screening in 2 weeks for the adaptyv nipah virus competition: Nipah Binder Competition Submission 1 To Get More Effective Drugs, We Need More Human Trials RFDiffusion3 is out: RosettaCommons/foundry Sterilization and contraception increase…
Periodic Table of Antibodies Computer Scientist’s Guide to Cell Biology Just know stuff, proteinML edition Retro bio clinical trial (1st one): ANZCTR Trial Registration
Boltzgen deep dive: Anatomy of BoltzGen Cradle Bio guy reading list: Just know stuff, proteinML edition Design comp (Ends December 1): Nipah Binder Competition IF1 Protein Controls Aging Rate Somatic mutations impose an entropic upper bound on human lifespan
From Lada Nuzhna’s trilly biotech post: Advancing gene-editing platforms to improve the viability of rare-disease therapeutics: key insights from a 2024 Scientific Exchange hosted by ARM, ISCT, and Danaher First-In-Human Therapy Stem Cell Dopaminergic Progenitor Parkinson’s Infant with rare, incurable disease is first to successfully receive personalized gene therapy treatment Personalized…
RFantibody, Github The Desci $50k
Chinese peptides, Everyone has a Chinese peptide dealer now More Chinese peptides, Tech bro’s manual for living forever Finnrick: Testing for Chinese peptides What should Finnrick test text? (posted on /r/saferpeptides
Let’s implement some attention modules. The 3Blue1Brown video on attention is really good for intuition. Sebastian Raschka’s “Build a Large Language Model” is really nice too for more in-the-weeds implementation details without any tricky math. Here’s the intuition: we’ve got some sequence; say it’s the sentence “the quick brown fox jumps over the…
It’s not obvious to me prima facie how tensor.T would be expected to work for tensor shapes of more than 2d, i.e. len(tens.shape) > 2. It turns out that the transpose occurs across the entire tensor, so if tens has shape (x, y, z) then tens.T has shape (z, y, x). Furthermore, tens[i, j, k] = tens[k, j, i]. I haven’t found it as intuitive geometrically to think about the transpose for…
Accept the mission Be humble Don’t mourn your flaws and shortcomings Be thankful for what you have Be thankful for the opportunity Be courageous Be resilient Remember the why Resist short-term temptation Act with urgency, but be patient
Jensens’ inequality says that for convex function $f(x)$ and random variable $X$, $f(E[X]) \le E[f(x)]$. (And conversely, for concave $f$, the reverse relationship holds). A good way to remember the direction of the inequality is by picturing the graphs below. (Thanks to Cursor and Codex for help with the Matplotlib charts, code reproduced below.) import matplotlib.pyplot as plt import numpy…
Variational (as in variational inference, variational autoencoder, etc) is an unintuitive term. You can read it as choosing a good function (typically a probability distribution) from some set of functions. The term comes from “calculus of variations,” which deals with optimization problems that involve choosing a best function (as opposed to e.g. choosing the best values for…
If you’re working in a project which relies on conda installs for system dependencies but you also want to use uv instead of pip for much faster python-only dependencies: You can create a new conda env the usual way (conda create -n whatever), then pip install uv. Now you can install python deps with uv pip install .... Thanks to Brandon Young for this tip.
Google released an API for their 2-way dialog model, the same technology that powers the podcast generation feature in NotebookLM. API docs here. It supports only 2 speakers. The dialog is represente as a series of speaking turns, each of which is assigned a speaker. There are 2 male and 2 female speakers supported, no custom voice or voice clones as of today. The model outputs are extremely…
Sometimes it feels like superhuman text to speech (and generative audio in general) is solved. But it’s not—even though TTS models are close or even superior to average humans in tasks like audiobook narration, they’re still way worse than the best humans in most speech domains. What follows is a collection of links that I believe represent the highest level of human speech generation.…
My experience with startups is that joy scales with growth rate and misery scales with headcount. That joy scales with growth rate is kind of obvious and likely needs no explanation. That misery scales with headcount seems to be because the more employees you have, the more frustrating personnel management and interpersonal conflict type issues you are bound to encounter. So for maximum happiness,…
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Now is a good time to start a service business. Maybe you should try it! A service business is one where your company sells its work output directly instead of selling a product. Dentists, plumbers, design agencies, pool cleaner, consultants: these are all service businesses. The opposite of a service business is a product business, where your company develops a product and sells it to customers.…
Today, a short tale of fun mystery-solving. I’ve been working on a project that involves a server dynamically generating audio files and streaming them to a client via a WebRTC session. The dynamic audio generation process works like this: first run a program that generates a wav file. Then compress the .wav to an .ogg which contains an Opus audio stream and deliver it over the network. The…
A small, cool fact about SQLite is that its columns are flexibly typed. You can store any value in any column! Try it out: sqlite> create table t1 (v1 int, v2 varchar(10)); sqlite> insert into t1 values ('abc', 'this string is longer than 10 characters!'); sqlite> select * from t1; abc|this string is longer than 10 characters! sqlite> select typeof(v1), typeof(v2) from t1; text|text The null type…
A list of useful or entertaining allegories about work. The Chicken and the Pig If a chicken and pig open up breakfast restaurant called Ham ‘N Eggs, the pig is totally committed but the chicken is merely involved. The Gervaise Principle The workplace consists of The Clueless, The Sociopaths, and The Losers. Barrels and Ammunition Employees are either barrels or ammunition. Ammunition…
Zach Wener is a software engineer and writer. You’re on his personal website. Thanks for the visit!
Three months ago, the college fiscal crisis was a fringe issue. Enrollment was already dropping, sure; but the brand-name schools didn’t seem to be affected and the colleges that had to shut their doors were either tiny, mostly-unknown liberal arts colleges or for-profits. No worries; Pura Vida. Three months ago, there were plenty of remote workers. Remote work grew steadily, but mostly at…
I recently came across a gem of an idea in a Douglas Crockford interview with Peter Seibel, from Seibel’s Coders at Work. The idea is that of a code reading: a public presentation of code that’s a sort of cross between a code review and a tech talk and a whiteboard session. As Crockford tells it, code readings sound pretty awesome: the mentorship effect of a great code review,…
I’ve got a proposal for an alternative to the dreaded technical interview loop that could make life easier, better and cheaper for people and their companies. The idea came from a conversation with coworkers I overheard a few years back: INT. OPEN OFFICE - DAY Two software engineers, GEORGE, a senior engineer and highly-skilled technical leader who people love to work with, and JOHN, a…
So you want to putter around with some data using Jupyter Notebook, and you don’t want to be limited by your local machine’s specs or have your laptop fan sounding like a jet engine. Here’s a solution using Google Compute Engine that takes about 10 minutes to set up. Create the virtual machine. You can do this via the Google Cloud UI by following the tutorial here. There are a…