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/agents-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 | $0.01013 | $0.01013 |
| Opus 5 | $0.00507 | $0.00507 |
| Sonnet 5 | $0.00203 | $0.00203 |
| Haiku 4.5 | $0.00101 | $0.00101 |
Grade A, and why
braina AGENTS.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 yesterday.
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 — 62 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. Project Structure
/mcp: MCP server (braina_mcp.py) exposing 30+ tools for Frites/HOI analysis. Registered as an MCP server for Codex./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 (BrainHack 2026, Granger causality, master's thesis).
3. Core Libraries
- Frites (v0.4.0+): Single-trial functional connectivity and information-theoretical analysis.
- Key modules:
frites.conn(covgc, dfc, pid, ii, te, fit, ccf, spec),frites.simulations(StimSpecAR),frites.workflow(WfMi, WfStats, WfConnComod). - GitHub:
brainets/frites
- Key modules:
- HOI (v0.2.0+): Higher-Order Interactions analysis.
- Key metrics: Oinfo, GradientOinfo, InfoTopo, RedundancyMMI, SynergyMMI, RSI, DTC.
- GitHub:
brainets/hoi
- XGI (v0.7.0+): Hypergraph and higher-order network analysis.
- GitHub:
xgi-org/xgi
- GitHub:
4. Source of Truth & Expertise
- Examples first: Always consult
/examplesfor usage patterns before writing new code. - MCP tools as reference: Read
mcp/braina_mcp.pyfor canonical function signatures and parameter conventions. - Source code on GitHub: For implementation details, read
brainets/fritesandbrainets/hoisource code. - Papers: Read PDFs in
/papersfor theoretical background when needed.
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.
- yesterday First seen · 62 lines · 1,013 tokens per session scan A 3cb702c9bbb4
braina AGENTS.md is an instructions file published in the GitHub repository brainets/braina (5 stars, last pushed 3mo ago), licensed BSD-3-Clause. It adds 1,013 tokens to every session, about $0.0051 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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