Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/brainets/braina/gemini-mdgit clone --depth 1 https://github.com/brainets/brainaWhat 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 | $0.01269 | $0.01269 |
| Opus 5 | $0.00634 | $0.00634 |
| Sonnet 5 | $0.00254 | $0.00254 |
| Haiku 4.5 | $0.00127 | $0.00127 |
Grade A, and why
braina GEMINI.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 2d 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 — 80 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Project: braina (Brain Interaction Analysis)
1. Project Context & Purpose
- Goal: Analyzing complex neural interactions using Frites, HOI, and XGI toolboxes.
- Focus: Information Theoretical Analysis of electrophysiological data (fMRI, MEG, EEG, LFP, MUA).
- Organization: Institut de Neurosciences de la Timone (BraiNets), Marseille, France.
- Novice Mode: The user may be a novice in this domain. Explain mathematical concepts (entropy, mutual information, O-information, Granger causality) simply and verify all proposed code before recommending it.
2. Commands
# Verify environment (all core dependencies)
uv run check_env.py
# Run the verification test suite for Frites + HOI
uv run mcp/verify_libs.py
# Launch the MCP server standalone
uv run mcp/braina_mcp.py
# Run any example script (all use uv inline dependencies)
uv run examples/frites/conn/ex_conn_covgc.py
uv run examples/hoi/metrics/ex_oinfo.py
All scripts use uv with PEP 723 inline script metadata (# /// script blocks) for dependency management.
3. Project Structure
/mcp: MCP server (braina_mcp.py) exposing 30+ tools for Frites/HOI analysis./examples: ~50 Python example scripts organized by library:examples/frites/— AR models, connectivity, mutual information, statistics, simulations.examples/hoi/— Information theory, HOI metrics, tutorials, statistics.
/papers: Research papers forming the theoretical foundation./tutorials: Hands-on learning materials:multivariate_information_theory_frites_hoi_xgi/— Integrating frites, hoi, and xgi.seeg_ebrains_frites/— SEEG data analysis with frites.
/usecases: Real-world analysis scenarios.
4. MCP Server Tools (mcp/braina_mcp.py)
Tool categories:
- Data I/O:
inspect_data,read_pdf,load_data,save_data - Frites connectivity:
frites_conn_covgc,frites_conn_dfc,frites_conn_pid,frites_conn_ii,frites_conn_te,frites_conn_fit,frites_conn_spec,frites_conn_ccf - Frites workflows:
frites_wf_stats(WfStats),frites_wf_mi(WfMi),frites_wf_conn_comod(WfConnComod) - Frites simulation:
frites_sim_ar(StimSpecAR) - HOI metrics:
hoi_oinfo,hoi_gradient_oinfo,hoi_infotopo,hoi_redundancy_mmi,hoi_synergy_mmi,hoi_rsi,hoi_dtc,hoi_get_nbest_mult
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.
- 2d ago First seen · 80 lines · 1,269 tokens per session scan A b0f40feee4ce
braina GEMINI.md is an instructions file published in the GitHub repository brainets/braina (5 stars, last pushed 3mo ago), licensed BSD-3-Clause. It adds 1,269 tokens to every session, about $0.0063 per session on Opus 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.
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symkit-mcp CLAUDE.md
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arxiv-wiki AGENTS.md
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