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Getting started

Install Claude Code, sign in, add the Open Science Skills, and point it at a project. A one-time setup, with no prior command-line experience assumed.

Overview

The aim is a setup where an AI agent reads the files in a folder and runs reusable checks over them, instead of a chat window you paste into. You install Claude Code, add the Open Science Skills, and point it at a project. After that, checking a reference list, or testing whether a source supports a claim, is a single command.

These instructions use the terminal, which is the simplest way in. You can also run Claude Code in an editor like VS Code or JetBrains, or through the web and desktop apps. The steps below assume the terminal.

1

Install Claude Code

Claude Code is the AI tool that runs the skills. Install it with one command in your terminal:

# macOS, Linux, or WSL
curl -fsSL https://claude.ai/install.sh | bash

# Windows (PowerShell)
irm https://claude.ai/install.ps1 | iex

Other install options are in the docs at code.claude.com/docs. Check it worked with claude --version.

2

Sign in

Open a terminal and run:

claude

The first time, it walks you through signing in with your Claude account in the browser. After that it stays logged in.

3

Add the Open Science Skills

The reference and source-claim checks come from the Open Science Skills plugin. Register the marketplace and install it:

claude plugin marketplace add scdenney/open-science-skills
claude plugin install oss@open-science-skills

Restart Claude Code (or run /reload-plugins) so the skills load. To confirm, type /help and look for the oss: commands, such as /oss:citation-check.

4

Open a project and call a skill

Move into the folder you want to work in and start Claude Code there:

cd path/to/your/project
claude

Now you can run a skill two ways. By its slash command:

/oss:citation-check manuscript.md references.bib

Or just by asking in plain language, for example "check the references in manuscript.md against references.bib." Claude Code reads the files in the folder, so point it at real files.

5

Build a knowledge base optional

This step is only for the source-claim check, which reads your sources to see whether they support a claim. The reference check does not need it.

Keep each source's PDF in sources/og/ and a Markdown version in sources/md/, which is what the checker reads. The research-repo skill sets this folder structure up for you, and process-source converts a PDF to Markdown.

/oss:research-repo            # scaffold the sources/ folders
/oss:process-source paper.pdf # convert one PDF into the knowledge base