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/biosymphony/cryocore/agents-mdgit clone --depth 1 https://github.com/BioSymphony/cryocoreWhat 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 | $0.00945 | $0.00945 |
| Opus 5 | $0.00473 | $0.00473 |
| Sonnet 5 | $0.00189 | $0.00189 |
| Haiku 4.5 | $0.00094 | $0.00094 |
Grade A, and why
cryocore 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 — 75 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BioSymphony CryoCore Agent Guide
This repo is the public BioSymphony CryoCore control plane. It owns cryo-EM evidence production, map/model validation, heterogeneity review, and structural rendering lanes that should not be coupled to AI design runtimes.
Operating Rules
- Keep durable design docs in
docs/. - Keep campaign specs in
campaigns/<campaign-id>/. - Keep public-safe example manifests and tiny fixtures in
examples/. - Keep reusable module contracts in
modules/. - Keep tool and licensing posture in
references/software-registry.yamlanddocs/tooling-and-licensing.md. - Keep reusable scripts under
scripts/cryocore/. - Use
templates/linear-issue.mdwhen drafting tracker-neutral external-agent issues. - Record durable learnings (tool surprises, failed paths, provider gotchas, doctrine corrections) in
.cryocore-memory/in this checkout (gitignored, never committed) or in your harness's own memory store. See Agent Memory And Learnings for scope, exclusions, harness pointers, and the note shape atskills/cryocore/references/memory-note-template.md. - Do not store API keys, tokens, raw cryo-EM movies, maps, half-maps, private structures, unpublished sequences, model weights, license files, or heavy outputs in this repo.
- Store heavy outputs under ignored directories such as
.runtime/,artifacts/,outputs/, provider volumes, or secure local storage. - Treat ChimeraX as intentionally duplicated with Structure Factory: runtime-gated, noncommercial/commercial-license posture recorded per campaign, and never redistributed in this public repo.
Ownership Boundary
CryoCore owns:
- raw cryo-EM movie intake contracts
- motion correction, CTF, picking, classification, refinement, and map postprocessing plans
- map/model validation and atomic model build lanes
- heterogeneity and conformational-state evidence lanes
- ChimeraX/Coot/PyMOL/Blender/Mol* figure and review scaffolding
- provider-neutral cryo-EM execution contracts for local, RunPod, AWS Batch, SSH/HPC, and neocloud-style backends
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 · 75 lines · 945 tokens per session scan A 6e103b3921ab
cryocore AGENTS.md is an instructions file published in the GitHub repository BioSymphony/cryocore (5 stars, last pushed yesterday), licensed MIT. It adds 945 tokens to every session, about $0.0047 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.
Other instructions, from other repositories
asb-skill-collections CLAUDE.md
Instructions for HolobiomicsLab/asb-skill-collections, covering claude.md — asb metabolomics skills, install (claude code plugin) and use.
asb-skill-collections copilot-instructions.md
Instructions for HolobiomicsLab/asb-skill-collections: This repository publishes the ASB Metabolomics Skill Collection (collections/metabolomics/v2/): 5,859 evidence-grounded skills over 909 software tools for computational LC-MS/MS metabolomics, each derived from a peer-reviewed method paper.
bioinformatics-agent-skills AGENTS.md
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering agent integration & specification guide 🤖, 📌 supported agent host architectures, 🧪 skill frontmatter specification and 🔒 security & sandboxing.
bioinformatics-agent-skills CLAUDE.md
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering claude code project guidelines, project overview, development & validation commands and skill conventions.
structure-factory AGENTS.md
Instructions for BioSymphony/structure-factory, covering biosymphony structure factory agent guide, mission, how to drive a mission, compute available and orchestrators supported.
statlingo AGENTS.md
AGENTS.md instructions for bgreenwell/statlingo, covering agents.md for statlingo, 1. project overview & mission, 2. repository layout, 3. the canonical prompts system (prompts/) and prompt synchronization.