sci-brain: Instructions file for Claude Code

CLAUDE.md

sci-brain CLAUDE.md is an instructions file for Claude Code from QuantumBFS/sci-brain. It costs 1,547 tokens per session, scanned A, original, MIT.

A repository guide for sci-brain, a plugin that gives AI coding assistants structured workflows for literature research, idea generation, writing, review, and autonomous research. Its main components are instruction files and supporting scripts.

In plain words
What is it for?
Use it when modifying sci-brain’s skills, research workflows, advisor resources, knowledge files, or compatibility with supported coding assistants.
Why use it?
It explains the project’s purpose, architecture, skills, and migration rules so agents can work in the right part of the plugin.

Instructions file for Claude Code

Written for Claude Code: Claude Code plugin machinery. Also seen: mentions .claude-plugin; mentions CLAUDE.md; mentions subagents.

This is QuantumBFS/sci-brain's own configuration. It tells Claude Code how to work on sci-brain itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything sci-brain configures →

Reuse

Borrowing it

Nothing to install: this file belongs to QuantumBFS/sci-brain. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/QuantumBFS/sci-brain/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/QuantumBFS/sci-brain

Made for: Claude Code.

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README.md
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Per session 1,547 This file is loaded in full into every session.
When invoked 1,547 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.01547 $0.01547
Opus 5.5 $0.00619 $0.00619
Sonnet 5.5 $0.00309 $0.00309
Haiku 4.5 $0.00155 $0.00155

Measured 22d ago against content hash be6275350115, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

sci-brain 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 22d 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.

CLAUDE.md · 96 lines

How it starts

The opening of the file, as written. The whole thing — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Repository Guide

This is the canonical project guide for agents working in this repository. Claude Code reads it directly; AGENTS.md routes Codex, OpenCode, and pi here so the project description stays in one place.

Project Overview

sci-brain is a skill-based plugin for AI coding assistants (Claude Code, Codex, OpenCode, pi) that provides structured literature, ideation, writing, review, and autonomous-research workflows. It is not a traditional application — its main product is the set of SKILL.md interaction protocols and their supporting scripts and references.

Working on skills

The 16 skills in skills/ are listed with their trigger descriptions in README.md. Load only the entry point and supporting resources needed for the current task. Public names match their containing directory.

  • User entry points: brainstorm-ideas, survey, write-paper, review-paper, write-slides, autoresearch, know-me-better, create-advisor, dump-chat-history.
  • Supporting workflows: how-to-build-kb, how-to-download-ref, how-to-analyze-dialog, how-to-flow, how-to-review-figure, how-to-technical-writing, how-to-write-ideas-report.

Each description is one sentence starting with User trigger. Use when … or, for how-to-* skills, Agentic trigger. Use when …. scripts/validate_skills.py enforces the prefix; tests/test_repository_consistency.py enforces how-to-* ⇔ agentic and keeps the README tables identical to the descriptions. When moving resources, keep public names stable and each skill installable on its own.

autoresearch routes topics → db → validator → run from research/STATE.md. Its user-confirmed acceptance gates, attempt budgets, and sealed holdout are research invariants. Status questions are read-only. A tidy-up (references/tidy-up.md, helpers/tidy_attempts.py) packs attempts into their branches and writes research/ATTEMPTS.md without ending the campaign.

Read the full file on GitHub · 96 lines

Changes

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.

  1. 22d ago Changed · +2 lines · +40 tokens per session be6275350115
  2. 24d ago Changed · -41 lines · -2,623 tokens per session 5d392356765d
  3. 29d ago Changed · +7 tokens per session ba95c4180025
  4. 1mo ago Changed · +7 tokens per session c17b9a66e362
  5. 1mo ago Changed · +3 lines · +265 tokens per session 7c7be117ea8e
  6. 1mo ago Changed · +4 lines · +72 tokens per session f35e972bb818
  7. 1mo ago Changed · +12 lines · +334 tokens per session 15b881ada10b
  8. 1mo ago First seen · 116 lines · 3,445 tokens per session scan A d8b0e20d508e

Subscribe to this mod's changes

sci-brain CLAUDE.md is an instructions file published in the GitHub repository QuantumBFS/sci-brain (101 stars, last pushed 23d ago), licensed MIT. It adds 1,547 tokens to every session, about $0.0062 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 2026-08-30.

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