A set of research skills for reproducing papers from arXiv, a website where researchers share scientific papers, and for checking AI experiments.

Use it to reproduce research papers, debug runs using recorded evidence, compare experiments at matching training points, and prepare disciplined launches.

It helps catch implementation mistakes, weak comparisons, and poorly documented experiment results before they waste time or computing resources.

phd-skills — Plugin by fcakyon

Install

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.

Claude Code

/plugin marketplace add fcakyon/phd-skills

agentmods

npx agentmods add plugins/fcakyon/phd-skills/plugin

Clone the repo

git clone --depth 1 https://github.com/fcakyon/phd-skills

Made for: Claude Code.

Per session not measured What this adds to a session before it is invoked.

When invoked not measured Not applicable: nothing here is loaded into a session.

Security scan A 0 findings. Scan, not verified.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

phd-skills 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 2d 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.

plugin/.claude-plugin/plugin.json · 16 lines

What it actually says

{
  "name": "phd-skills",
  "version": "1.3.0",
  "description": "Catch AI mistakes before they cost weeks of compute. Reproduce papers from arxiv. Debug runs evidence-first. Compare experiments at the right epoch. Launch with discipline.",
  "keywords": [
    "research",
    "academic",
    "phd",
    "paper-reproduction",
    "debugging",
    "experiment-analysis",
    "citations",
    "latex"
  ]
}

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.

2d ago First seen · 16 lines scan A 75a35ec1c3e7

Subscribe to this mod's changes

phd-skills is a plugin published in the GitHub repository fcakyon/phd-skills (377 stars, last pushed 2mo ago), licensed MIT. Its token cost is not measured: this kind of file is read by the harness, not the model. 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.

Debugging Research Scientific academic agents ai claude-code phd

tooluniverse

1000+ scientific research tools for biology, chemistry, medicine, and data science. Access PubMed, UniProt, PubChem, TCGA, NHANES, GWAS Catalog, and hundreds more databases through a unified MCP interface. Includes 120+ specialized research skills for genomics, drug discovery, clinical analysis, protein variant…

mims-harvard/ToolUniverse · not measured

phd-skills

Getting it into your agent

Grade A, and why

Nothing flagged

What it actually says

What this file has done since we first saw it

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