Joshua Cook

The Illumina bioinformatics team reanalyzed the 1000 Genomes Project to establish a new analytical baseline for common human genetic variation.

My trip report from backpacking and fishing in the Golden Trout Wilderness in the Sierra Nevada with a friend from graduate school.

Working in a ‘uv’ Workspace brings complication and overhead, but here I provide four real-life use cases that this mono-repo style makes more manageable.

I document my first trial run of a non-trivial agent with a multi-step task.

This is the beginning of what I hope will be a series of posts about using the DeepAgents library to build powerful AI agents.

My thoughts after one week of thoroughly using Cursor AI coding environment on real projects at work.

A project at work to re-analyze the 1000 Genomes Project individuals and trios with the latest version of DRAGEN.

This is just a quick post about a way I found in graduate school to quickly delete large amounts of data.

Between 2025 and 2026, I read the original James Bond series by Iam Fleming and then watched the canonical movie series.

Reviews of the books I read in 2026.

Python implementations for some of the algorithms covered by Algorithms in Bioinformatics by Wing-Kin Sung.

My experience taking on the Western Native Trout Challenge to explore the greatest waters in the country.

In persuit of the out-of-stock Colter Thorofare Net, I quickly created a GitHub Action to email me when it appeared back in-stock.

A quirky watch that flies under the radar.

Reviews of the books I read in 2025.

A review of my favorite books of the year and why I particularly enjoyed them.

This is a short post to introduce a tool for Jupyter notebooks called ‘watermark.’

A great way to clear my mind and challenge myself.

Adventure is out there!

Such a great excuse to be outside and interact with nature.

My admiration of history, brilliant engineering, and eye-catching design.

My admiration of history, brilliant engineering, and eye-catching design.

My reasons and methods for learning the Rust programming language.

Hobby project to try to identify books and authors on a bookshelf.

The steps I have taken to learn how to conduct Bayesian data analysis.

I love the variety of cacti and succulents, there is always more to learn and see.

This is a description of how I use Python in my data analyses, a system that has evolved over 7 years of a computational biology Ph.D. and working in industry.

Spreading out computation is made simple in Python with the built-in multiprocessing module.

Everyone loves bread.

In the course of my work, I stumbled across a misconception I had about the Final type annotation.

A story of how symptoms in my Pi-hole lead me to diagnose that my Raspberry Pi was under-powered.

A list of my favorite productivity, software development, and personal applications on my MacBook.

A simple tutorial for getting up and running with LLMs running on your local computer.

Reviews of the books I read in 2024.

A review of my favorite books of the year and why I particularly enjoyed them.

Pushing Rust projects to Deta can require cross-compiling or timeout during the build process.

A simple introduction to generic type hints in Python and how to use them in classes.

This links to my repository of #TidyTuesday submissions.

Reviews of the books I read in 2023.

A review of my favorite books of the year and why I particularly enjoyed them.

I provide a simple example of a Dirichlet regression in PyMC.

The NCI Ras Initiative’s Ras Pathway 2.0 exposed as a NetworkX object.

Tumoroscope, a generative model of spatial transcriptomics clonality, implemented in PyMC.

Automatically download and parse research articles then summarize them with various ML and AI models.

I experimented with different structures for multi-level and hierarchical splines in PyMC, including using a multivariate normal prior distribution over the spline parameters.

Does the warning ‘Using NumPy C-API based implementation for BLAS functions’ from Theano when using PyMC3 affect the performance of MCMC?

Modeling the standard curve of a standard dilution experiment with Stan as presented in Bayesian Data Analysis by Gelman et al.

My simple application to put oft copied text in easy reach in my Mac’s menu bar.

How to support type hints of the dunder methods on your subclass of the built-in Python list using function overloading.

A step-by-step tutorial on how to get a powerful backend system up and running on Digital Ocean.