Borrowing it
Nothing to install: this file belongs to BioSymphony/structure-factory. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/BioSymphony/structure-factory/main/AGENTS.mdgit clone --depth 1 https://github.com/BioSymphony/structure-factoryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/biosymphony/structure-factory/agents-md)<a href="https://agentmods.dev/instructions/biosymphony/structure-factory/agents-md"><img src="https://agentmods.dev/badge/instructions/biosymphony/structure-factory/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/biosymphony/structure-factory/agents-md"><img src="https://agentmods.dev/badge/instructions/biosymphony/structure-factory/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.01404 | $0.01404 |
| Opus 5.5 | $0.00562 | $0.00562 |
| Sonnet 5.5 | $0.00281 | $0.00281 |
| Haiku 4.5 | $0.00140 | $0.00140 |
Grade A, and why
structure-factory 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 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.
How it starts
The opening of the file, as written. The whole thing — 112 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BioSymphony Structure Factory Agent Guide
Use this repository to write and check structural biology campaign contracts, task packs, provider plans, and result records.
Mission
Turn a target, accession, or screening request into files that another agent or scientist can inspect and continue.
The repo ships:
- portable agent instructions for any agent runtime
- campaign manifests, stage contracts, and provider profiles for RunPod, AWS, FAL, Modal, Lambda, neocloud, HPC, and local
- target-window files, generation, cofold, scoring, render, and screening lanes
- tracker-neutral task packs for Linear, GitHub Issues, Notion, or another queue
- validators, audit gates, capability catalog, and a dependency-free
bsfCLI
Ownership boundary: raw cryo-EM movie intake, EMPIAR subset execution, RELION or CryoSPARC reconstruction, and map-to-model build execution belong to BioSymphony CryoCore. This repo keeps public metadata, handoff gates, downstream structure-mapping contracts, validation plans, and reviewable summaries.
How To Drive A Mission
When the orchestrator hands you work, the loop is:
goal
-> bsf catalog . # what is available
-> bsf scaffold-campaign <runtime>/<id> ... # target, lanes, run boundaries
-> bsf validate <runtime>/<id> # campaign and stage contract sound
-> bsf issue-dry-run # split into tracker work
-> orchestrate workers or launch provider # Symphony, Linear, Codex, others
-> verify artifacts and sign closeout
Use multiple workers only when the task pack assigns separate paths, dependencies, validation commands, and outcomes.
Provider Contract Coverage
- Local: a workstation profile for planning and fixtures.
- RunPod: pod profiles and public launch-contract templates.
- AWS: Batch and EC2 GPU profiles.
- FAL: a serverless GPU-job profile.
- Modal: a serverless GPU-function profile.
- Lambda Cloud: an ephemeral GPU-VM profile.
- Neocloud and generic cloud: GPU pod or VM profiles.
- SSH or HPC: a Slurm-oriented profile.
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.
- 1mo ago Changed · -3 lines · -206 tokens per session f1693a7f5451
- 1mo ago First seen · 115 lines · 1,610 tokens per session scan A 0c9b0500ad8d
structure-factory AGENTS.md is an instructions file published in the GitHub repository BioSymphony/structure-factory (13 stars, last pushed 12d ago), licensed MIT. It adds 1,404 tokens to every session, about $0.0056 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.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.