Oxford Protein Informatics Group

How to start?

Start with the `CLAUDE.md` file. It’s a special file Claude reads at the start of every conversation, and it’s where you define the behaviour of the agent (other agents have their own equivalent — for example `AGENTS.md`). In this file, include things like bash commands, code style preferences, and workflow rules. This gives Claude a persistent context that it can’t infer from the codebase alone.

What is a tool?

A tool gives the agent a capability. It executes an action and returns a result — calling an API, running code, querying a database, and so on. The key idea is that tools are deterministic: given the same input, they produce the same output. So if I ask, “Can you check whether this is an antibody?”, the agent will always reach for the same tool — `execute_run_anarci()` — and get the same result.

What is a skill?

Skills extend Claude with procedural knowledge. They teach the agent how to perform a task, not just what tools are available. I think of tools as capabilities and skills as workflows. Tools let the agent do something; skills tell it how to approach a task. A tool might tell Claude how to number an antibody sequence.