Personalized peptides for respiratory viruses
Nasal sprays and personalized peptide binders for respiratory viruses.
Boolean Biotech
Latest posts
VHH design competition results and easymosaic
VHH competition results and easymosaic
Oral microbiome sequencing after taking probiotics
Analysis of my oral microbiome after taking a probiotic.
Using Claude Code for computational biology
A short case study of using Claude Code with Opus 4.5 for a computational biology task
Boolean Biotech VHH Design Competition 2025
Boolean Biotech VHH Design Competition 2025
AI antibody design in 2025
A review of antibody design tools
AI and protein patents
A review of protein patents and the impact of AI
Protein binder design revisited
A review of protein binder design
A list of health-related products
A list of health-related products
What we learned about binder design from the Adaptyv competition
What we learned about binder design from the Adaptyv competition
The ABCs of Alphafold 3, Boltz and Chai-1
Comparing Alphafold 3, Boltz and Chai-1
The Adaptyv binder design competition
Some notes on the Adaptyv binder design competition
A simple evolution simulation
A simulation of evolution and predator–prey dynamics
Evaluating longevity drugs with LLMs
Using LLMs to search PubMed and summarize information on longevity drugs.
Progress towards parsing publications with LLMs
Using LLMs to search pubmed and summarize information.
Using modal for bioinformatics
An example and examination of using modal for bioinformatics
A simple way to simulate protein–ligand interactions (that does not work)
Molecular dynamics code for protein–ligand interactions
Colab and computational tools for drug design
Using colab to chain computational drug design tools
Using GPT-3 as a knowledge-base in biotech
Using GPT-3 as a knowledge-base for a biotech
Computational tools for drug development
Computational tools for drug development
The baffling COR
Trying out The COR, a home blood diagnostic device.
Modern biotech data infrastructure
Some notes on setting up data infrastructure for a new biotech.
Permutation tests are good
Some examples of permutation tests being applied to t-test-like problems.
Sequencing a human genome at home
Sequencing a human genome at home, using a nanopore sequencer.
Modeling EV range with a multilevel model
Using Bambi and brms to estimate the efficiency of electric cars.
Numpyro probabilistic model of blood glucose
Numpyro probabilistic model of blood glucose
Water purity analysis with a GeneQuant
Using a GeneQuant to measure water purity
A month with a CGM: an analysis of blood glucose responses to food
Using a CGM to test the effect of foods on blood glucose.
DNA sequencing at home with the flongle
DNA sequencing at home using Oxford Nanopore's new flongle sequencer.
Comparing bioinformatics workflow systems: nextflow, snakemake, reflow
A brief comparison of three bioinformatics workflow tools: nextflow, snakemake, reflow.
Tools for working on the cloud
A list of tools for working remotely on a cloud instance.
Instagram celebrity generation using neural nets: Jake Dangerback
Using several neural nets to create an instagram celebrity, Jake Dangerback.
The Sequencing Gap
Sequencing gap
The amyloid hypothesis
A review of the amyloid hypothesis in Alzheimer's and some recent drug trials.
DNA alignment with Python, Nim and JavaScript
Implementing Needleman-Wunsch a few different ways in Python, Nim, and JavaScript.
Normal-looking distributions and maximum entropy
Deriving the normal distribution and others using maximum entropy.
Y Combinator and Biotech, 2017
A brief look at Y Combinator's biotech investments in 2017.
Drug Targets and Therapies
Some notes on drug development: classes of drug targets and therapies.
An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake
How to automate protein synthesis pipeline using transcriptic and snakemake
Internet of Lab Things
An internet-connected lab thermometer
Oxford Nanopore in 2016
What's been going on with Oxford Nanopore in 2016
A Toy Oxford Nanopore Simulator Using A Hierarchical Bayesian Model in PyMC3
Estimating parameters for a toy nanopore simulator using a hierarchical Bayesian model in PyMC3
Cool Things Review
A review of interesting things in biotech, genomics, data analysis
Convolutional Neural Net Playing a 3D Game
Convolutional neural net playing a 3D game using convnetjs and three.js
Engineering Proteins in the Cloud with Python and Transcriptic, or, How to Make Any Protein You Want for $360
A genetic engineering pipeline entirely in Python
Transcriptic pUC19 PCR Amplification
Amplifying pUC19 on Transcriptic
IPython Notebook Tips
Some useful IPython notebook tips.
Transcriptic E. coli Transformation
Transforming an E. coli with luciferase on Transcriptic and measuring the result
The Modern Virtual Biotech
Describing how a modern virtual biotech might work
Arcturus BioCloud Robot Lab
Arcturus' platform for synthetic biology