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/elliotxie/autozyme/claude-mdgit clone --depth 1 https://github.com/ElliotXie/autozymeWrote 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/elliotxie/autozyme/claude-md)<a href="https://agentmods.dev/instructions/elliotxie/autozyme/claude-md"><img src="https://agentmods.dev/badge/instructions/elliotxie/autozyme/claude-md.svg" alt="Measured on agentmods" 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 | $0.00289 | $0.00289 |
| Opus 5 | $0.00144 | $0.00144 |
| Sonnet 5 | $0.00058 | $0.00058 |
| Haiku 4.5 | $0.00029 | $0.00029 |
Grade A, and why
autozyme 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 5d 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.
What it actually says
autozyme
Autonomous CPU-side speed optimization of scientific computing functions. One target function per task; iterate via the zyme CLI.
Layout
autozyme_cli/— the CLI framework. Install withpip install -e autozyme_cli/.autozyme_py/— Python accelerator package (ships optimized patches).autozyme_r/— R accelerator package (ships optimized patches).datasets/— README + setup scripts. Actual data on HuggingFace:elliotxie/autozyme-datasets.
How to use
pip install -e autozyme_cli/zyme --versionto verify- Follow
autozyme_cli/zyme/prompts/Bio/0_bootstrap.mdto start a new optimization task
Environment
- R tasks (Seurat, Bioconductor): need R + relevant packages installed.
- Python tasks (Scanpy, etc.): need conda env with the target package.
- Data: downloaded from HuggingFace by the init agent when needed.
CLI quick reference
zyme init <repo> [<function>] # scaffold a task
zyme run "<hypothesis>" # run an optimization attempt
zyme accept / reject # keep or discard
zyme status # task state summary
zyme verify # thread x tier validation matrix
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.
- 5d ago First seen · 33 lines · 289 tokens per session scan A 6538b8ff8bba
autozyme CLAUDE.md is an instructions file published in the GitHub repository ElliotXie/autozyme (49 stars, last pushed 20d ago), licensed MIT. It adds 289 tokens to every session, about $0.0014 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 2026-08-30.
Other instructions, from other repositories
mosaicatcher-pipeline CLAUDE.md
Claude Code instructions for friendsofstrandseq/mosaicatcher-pipeline, covering claude.md, project overview, version management, common commands and using pixi (recommended for snakemake v9+).
precision-medicine-mcp CLAUDE.md
Instructions for lynnlangit/precision-medicine-mcp, covering claude.md — project context for claude code, git workflow, session management, what this project is and repository structure.
opentargets-mcp AGENTS.md
Instructions for nickzren/opentargets-mcp, covering agent guide — opentargets-mcp, what this server is, run locally (stdio), use this server for and triage hints.
open-genome-agent AGENTS.md
Instructions for 45ck/open-genome-agent, covering agents.md, core policy, mission, mandatory rules and delegation rules.
mosaicatcher-pipeline GEMINI.md
Gemini CLI instructions for friendsofstrandseq/mosaicatcher-pipeline, covering claude.md, project overview, version management, common commands and using pixi (recommended for snakemake v9+).
mygene-mcp AGENTS.md
AGENTS.md instructions for nickzren/mygene-mcp, covering agent guide — mygene-mcp, what this server is, run locally (stdio), use this server for and triage hints.