asb-skill-collections: Instructions file for GitHub Copilot

.github/copilot-instructions.md

asb-skill-collections copilot-instructions.md is an instructions file for GitHub Copilot from HolobiomicsLab/asb-skill-collections. It costs 395 tokens per session, scanned A, original, Apache-2.0.

A set of evidence-based skills for computational LC-MS/MS metabolomics, a method for measuring and identifying small molecules in biological samples. Each skill is based on a peer-reviewed research paper and covers a software tool or analysis method.

In plain words
What is it for?
Use it to find metabolomics skills by scientific topic, software tool, or EDAM identifier, then follow the linked method instructions and source-paper checks.
Why use it?
It helps agents locate relevant analysis methods and verify technical claims against scientific sources instead of guessing.

Instructions file for GitHub Copilot

Written for GitHub Copilot: a Copilot instructions file. Also seen: mentions AGENTS.md.

This is HolobiomicsLab/asb-skill-collections's own configuration. It tells GitHub Copilot how to work on asb-skill-collections 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 asb-skill-collections configures →

Reuse

Borrowing it

Nothing to install: this file belongs to HolobiomicsLab/asb-skill-collections. 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/HolobiomicsLab/asb-skill-collections/main/.github/copilot-instructions.md
Clone the repo
git clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collections

Made for: GitHub Copilot.

Wrote 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.

agentmods badge for asb-skill-collections copilot-instructions.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/holobiomicslab/asb-skill-collections/copilot-instructions/github.svg)](https://agentmods.dev/instructions/holobiomicslab/asb-skill-collections/copilot-instructions)
Your own site
<a href="https://agentmods.dev/instructions/holobiomicslab/asb-skill-collections/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/holobiomicslab/asb-skill-collections/copilot-instructions/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.

agentmods 80×15 button for asb-skill-collections copilot-instructions.md

Your own site · 80×15
<a href="https://agentmods.dev/instructions/holobiomicslab/asb-skill-collections/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/holobiomicslab/asb-skill-collections/copilot-instructions.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 395 This file is loaded in full into every session.
When invoked 395 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 $0.00395 $0.00395
Opus 5.5 $0.00158 $0.00158
Sonnet 5.5 $0.00079 $0.00079
Haiku 4.5 $0.00040 $0.00040

Measured 1mo ago against content hash 07ebc387875f, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

asb-skill-collections copilot-instructions.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.

.github/copilot-instructions.md · 27 lines

What it actually says

GitHub Copilot — ASB Metabolomics skills

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.

Read AGENTS.md for the full install + use protocol. In short:

  • Skills are plain Markdown at collections/metabolomics/v2/leaves/<slug>/SKILL.md (only skills/_router, the asb-metabolomics licence gate and the asb-contribute contribution route sit under skills/, because a plugin host advertises everything there into the session prompt) (YAML frontmatter + body). The entry point is skills/_router/SKILL.md.
  • To find a skill, search the indexes at collections/metabolomics/v2/: skills_index.json (by EDAM IRI, tool name, or keyword over name/description) and tools_index.json. Prefer EDAM/tool matches over keyword.
  • To apply a skill, open its SKILL.md and follow the procedure; the frontmatter tools + tools_index.json give canonical install URLs.
  • To verify a claim/parameter, ground it against the source paper with scripts/perspicacite_kb_bind.py query --collection collections/metabolomics/v2 --skill <slug> --question "..." (the skill→paper KB map is in kb_bundle.json).

When suggesting metabolomics analysis code, prefer the tools and procedures these skills describe, and cite the skill's derived_from DOI. The public release is metabolomics only; ignore other domains under collections/.

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 · +1 lines · +16 tokens per session 07ebc387875f
  2. 1mo ago First seen · 26 lines · 379 tokens per session scan A e25b8700b891

Subscribe to this mod's changes

asb-skill-collections copilot-instructions.md is an instructions file published in the GitHub repository HolobiomicsLab/asb-skill-collections (16 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 395 tokens to every session, about $0.0016 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.

Related

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).

microsoft/vscode · 9,649 tokens

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.

vercel/next.js · 7,384 tokens

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).

microsoft/vscode · 5,262 tokens

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.

langchain-ai/langchain · 4,680 tokens

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).

microsoft/vscode · 2,731 tokens

deno copilot-instructions.md

Copilot instructions for denoland/deno, covering deno development guide for github copilot, network access, high level overview, key directories and key files to understand first.

denoland/deno · 3,077 tokens