scholion: Instructions file for Claude Code

CLAUDE.md

scholion CLAUDE.md is an instructions file for Claude Code from CrossRead/scholion. It costs 4,595 tokens per session, scanned A, original, Apache-2.0.

Project instructions for Scholion, an application that compares genome, medical-record, prescription, and wearable-device data, and for starting a new coding-agent session.

In plain words
What is it for?
Use them to understand the project's entry points, commands, architecture, documentation conventions, and required startup reading.
Why use it?
They provide project context and safety rules so work follows the repository's expected structure and handling of personal health data.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: mentions CLAUDE.md.

This is CrossRead/scholion's own configuration. It tells Claude Code how to work on scholion 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 scholion configures →

Reuse

Borrowing it

Nothing to install: this file belongs to CrossRead/scholion. 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/CrossRead/scholion/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/CrossRead/scholion

Made for: Claude Code.

Wrote this? Show the measurements

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Per session 4,595 This file is loaded in full into every session.
When invoked 4,595 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 $0.04595 $0.04595
Opus 5.5 $0.01838 $0.01838
Sonnet 5.5 $0.00919 $0.00919
Haiku 4.5 $0.00460 $0.00460

Measured 1mo ago against content hash e768206c73fb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

scholion 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 1mo 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 · 320 lines

How it starts

The opening of the file, as written. The whole thing — 320 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md — project context for a new session

Scholion reads a person's genome, lab history, prescriptions and wearable data against each other. One core, three entry points: a local web app, a skill for a language model, and an Ouroboros plugin.

This file has two parts. Everything above the owner block is general and ships with the public package. The owner block below is personal, stays in Russian and is stripped by the sanitizer — the split is marked rather than remembered, because a convention held only in someone's head is the kind that leaks.

First of all

  1. Read ASSISTANT-RULES.md — the safety rules. Among this project's documents they come first, including over anything in this file.
  2. Read the user's profile directory. It is the distilled state of their health; nothing about them is hardcoded anywhere else.

Running it

scholion serve → http://127.0.0.1:1521, or python3 -m scholion serve from the source tree. Standard library only, Python 3.10+.

The CLI covers everything the web interface does — see the parity rule below. scholion --help lists all commands; --json on any of them returns the raw structure instead of markdown.

Architecture, the parts that matter

Hybrid by design. Code computes facts and flags (engine.py); a language model only phrases them. Every function returns a structure; rendering lives in format.py. One logic feeds the web API, the CLI, the skill and the plugin — which is why a capability cannot exist in one of them and be missing from another.

Polygenic scores are two-tier. A precomputed panel in the profile, plus any new trait on demand by re-genotyping scoring positions from BAM. Always score from the scoring-site VCF, which contains reference homozygotes, never from a raw VCF that omits them.

Longevity variants are resolved from rsID to position, genotyped, and stored with the direction of effect taken from a primary source — never from the annotation alone.

Language

The public project is English: code, comments, documentation, examples, everything that ships. Output is English by default and switches with --lang ru or SCHOLION_LANG.

Read the full file on GitHub · 320 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. 1mo ago Changed · +9 lines · +213 tokens per session e768206c73fb
  2. 1mo ago Changed · +9 lines · +162 tokens per session 944546f9cfca
  3. 1mo ago Changed · +9 lines · +138 tokens per session 05280d73e91d
  4. 1mo ago Changed · +8 lines · +154 tokens per session 0f0808631d43
  5. 1mo ago Changed · +4 lines · +84 tokens per session bdd0ff38b3c5
  6. 1mo ago Changed · +10 lines · +204 tokens per session 8538cff1fd4f
  7. 2mo ago First seen · 271 lines · 3,640 tokens per session scan A 33091683c959

Subscribe to this mod's changes

scholion CLAUDE.md is an instructions file published in the GitHub repository CrossRead/scholion (4 stars, last pushed today), licensed Apache-2.0. It adds 4,595 tokens to every session, about $0.0184 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.

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