Notes
AI & computational biology, with code
Working notes on applying LLMs, agents, and foundation models to bioinformatics workflows. Every post links to a runnable GitHub repo.
Three ways an LLM in the loop breaks reproducibility
A bioinformatician's view: the decision trail, the opaque code trail, and layered non-determinism, the three reproducibility problems that are new when an LLM writes (or runs) your analysis.
How to install a Claude Code Skill — Methods drafter walkthrough
How to install a Claude Code Skill at ~/.claude/skills/<name>/SKILL.md so every future Claude Code session loads it automatically — no re-pasting. Methods drafter walkthrough.
How to add a reusable Python tool to Claude — PubMed search example
How to add a reusable Python tool Claude can call from any notebook or claude CLI session. PubMed search walkthrough with the install pattern.
How to write your first Claude Code Skill — Methods drafter example
How to write your first Claude Code Skill — a persistent rule Claude loads automatically. Methods section drafter walkthrough, with the full SKILL.md.
Set up the Claude API on macOS or Linux — venv, API key, .env
Set up the Claude API on macOS or Linux: Python venv with the Anthropic SDK, an API key from console.anthropic.com, and a .env file. Cost notes and troubleshooting included.