Borrowing it
Nothing to install: this file belongs to brainets/braina. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/brainets/braina/main/CLAUDE.mdgit clone --depth 1 https://github.com/brainets/brainaWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/brainets/braina/claude-md)<a href="https://agentmods.dev/instructions/brainets/braina/claude-md"><img src="https://agentmods.dev/badge/instructions/brainets/braina/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/brainets/braina/claude-md"><img src="https://agentmods.dev/badge/instructions/brainets/braina/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.01700 | $0.01700 |
| Opus 5.5 | $0.00680 | $0.00680 |
| Sonnet 5.5 | $0.00340 | $0.00340 |
| Haiku 4.5 | $0.00170 | $0.00170 |
Grade A, and why
braina CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 29d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 90 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
Project Overview
Braina is an AI-agent-assisted framework for analyzing complex neural interactions using information-theoretical measures on electrophysiological data (fMRI, MEG, EEG, LFP, MUA). Built at the Institut de Neurosciences de la Timone (BraiNets), Marseille.
The user may be a novice in computational neuroscience. Explain mathematical concepts (entropy, mutual information, O-information, Granger causality) simply and verify all proposed code before recommending it.
Commands
# Verify environment (all core dependencies)
uv run check_env.py
# Run the verification test suite for Frites + HOI
uv run plugin/mcp/verify_libs.py
# Run the pytest suite over all MCP tools (synthetic data, ~30 s)
uv run tests/run_tests.py
# End-to-end smoke test of the installation (what /braina:check runs)
uv run plugin/scripts/smoke_test.py
# Launch the MCP server standalone
uv run plugin/mcp/braina_mcp.py
# Refresh the server lockfile after editing its dependency block
uv lock --script plugin/mcp/braina_mcp.py
# Behavioural evals of the skills
claude plugin eval plugin
# Run any example script (all use uv inline dependencies)
uv run plugin/examples/frites/conn/plot_covgc.py
uv run plugin/examples/hoi/metrics/plot_oinfo.py
All scripts use uv with PEP 723 inline script metadata (# /// script blocks) for dependency management — no virtualenv setup needed.
Architecture
Repository layout
Everything the plugin installs lives under plugin/ (manifest, MCP server + lockfile, skills, examples, hooks, scripts, evals); the marketplace points at it (.claude-plugin/marketplace.json, source: ./plugin). Papers, tutorials, use cases, tests and CI stay at the root and are not installed.
MCP Server (plugin/mcp/braina_mcp.py)
The central integration layer. A FastMCP server exposing 34 tools that wrap Frites and HOI library functions with standardized file-based I/O. Each tool takes file paths as input (.npy or .nc), calls the underlying library function, saves results, and returns a text summary (shape, coords, min/mean/max). Exceptions are caught and returned as Error in <tool>: ... strings. The server is declared in plugin/.claude-plugin/plugin.json under mcpServers; plugin/hooks/hooks.json pre-warms its uv environment at session start. This is registered as a Claude Code MCP server (braina).
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 29d ago Changed · +24 lines · +683 tokens per session fd376404f00f
- 1mo ago Changed · +31 tokens per session cb4897fbee81
- 1mo ago Changed · -1 lines · -94 tokens per session dd395f3bfe22
- 1mo ago First seen · 67 lines · 1,080 tokens per session scan A e91c67a28fd8
braina CLAUDE.md is an instructions file published in the GitHub repository brainets/braina (5 stars, last pushed 1mo ago), licensed BSD-3-Clause. It adds 1,700 tokens to every session, about $0.0068 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.