my-academic-skills: Instructions file for Codex

AGENTS.md

my-academic-skills AGENTS.md is an instructions file for Codex, OpenCode from SPYfighting/my-academic-skills. It costs 574 tokens per session, scanned A, original, MIT.

Repository instructions for SPYfighting/my-academic-skills, including how to choose and use skills, how the repository is organized, and how to add or version them. It also defines checkpoints that require human approval in some protein-design workflows.

In plain words
What is it for?
Working with protein-binder, structure-prediction, and protein-design skills, adding repository skills, following version conventions, and checking required workflow gates.
Why use it?
It gives an agent consistent rules for finding the right scientific workflow, handling external identifiers, and stopping at required approval points.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md.

This is SPYfighting/my-academic-skills's own configuration. It tells Codex and OpenCode how to work on my-academic-skills 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 my-academic-skills configures →

Reuse

Borrowing it

Nothing to install: this file belongs to SPYfighting/my-academic-skills. 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/SPYfighting/my-academic-skills/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/SPYfighting/my-academic-skills

Made for: Codex, OpenCode.

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 my-academic-skills AGENTS.md

README.md
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Your own site
<a href="https://agentmods.dev/instructions/spyfighting/my-academic-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/spyfighting/my-academic-skills/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.

agentmods 80×15 button for my-academic-skills AGENTS.md

Your own site · 80×15
<a href="https://agentmods.dev/instructions/spyfighting/my-academic-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/spyfighting/my-academic-skills/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 574 This file is loaded in full into every session.
When invoked 574 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 $0.00574 $0.00574
Opus 5 $0.00287 $0.00287
Sonnet 5 $0.00115 $0.00115
Haiku 4.5 $0.00057 $0.00057

Measured yesterday against content hash c234cee3bedd, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

my-academic-skills 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.

AGENTS.md · 32 lines

How it starts

The opening of the file, as written. The whole thing — 32 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Repository conventions

This file governs changes to the repository. To use a skill, read its own SKILL.md; its domain rules apply to that workflow.

Find a skill

Request Entry point
Protein binder design, structure prediction, or protein engineering binder-design-campaign/SKILL.md
Editable scientific diagrams, raster reconstruction, or local Illustrator drawing scientific-illustrator-local/SKILL.md

Layout and writing

  • One skill per top-level directory, with matching directory name and name frontmatter. SKILL.md must also include a useful description.
  • Each skill is self-contained. Keep runtime instructions, scripts, fixtures, licenses, and required references inside it. Resolve paths relative to the skill root unless a link explicitly says otherwise.
  • Keep entry points concise. Put conditional detail in references/, workflows/, or other directories only when needed, with a clear pointer explaining when to read it.
  • Write skill instructions in English. Preserve the language of user-provided content such as figure labels. Use ASCII for diagnostic messages and UTF-8 for content files.
  • Prefer standard-library helpers. When a skill requires third-party packages or a native application, declare them in that skill, pin dependencies where appropriate, and make installation an explicit step.
  • Repository documentation covers discovery, installation, contribution, and attribution. Detailed scientific methods, application-specific limits, and review gates belong to their skill.

For substantial edits to agent-facing prose, use writing-for-agents when available. Keep one authoritative explanation of each rule and preserve source attribution. Changes to binder protocol prose must be reflected in its docs/source-mapping.md.

Add or change a skill

  1. Create or update the self-contained skill directory. Preserve existing behavior outside the requested scope.
  2. Provide scripts/selfcheck.py for automated validation. It should exercise representative valid input and reject meaningful invalid input, without opening native applications or making network requests. State what remains untested.
  3. Add or update one concise row in each README and the routing table above. Record version changes in CHANGELOG.md and CITATION.cff; a new skill is a minor repository release.
  4. Run python check.py with the required per-skill dependencies available. All selected skills must pass; an absent self-check is not a pass.
  5. Review the complete diff, then commit only the affected skill and related repository files. Publish through normal commits on the intended branch, preserving existing history.

Read the full file on GitHub · 32 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. yesterday Changed · -99 lines · -889 tokens per session c234cee3bedd
  2. 10d ago First seen · 131 lines · 1,463 tokens per session scan A 23f308cbeabd

Subscribe to this mod's changes

my-academic-skills AGENTS.md is an instructions file published in the GitHub repository SPYfighting/my-academic-skills (12 stars, last pushed yesterday), licensed MIT. It adds 574 tokens to every session, about $0.0029 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.

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