Medical Research Agent Skills is a library of agent instructions for medical and biomedical research, covering evidence analysis, study protocol design, data analysis, and academic writing. Researchers use it to guide compatible coding agents through common scientific workflows. The catalogue contains many of the library's skills and commands.
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 skills add aipoch/medical-research-skills --skill clinical-cohort-protocol-designergit clone --depth 1 https://github.com/aipoch/medical-research-skillsWrote 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/skills/aipoch/medical-research-skills/clinical-cohort-protocol-designer)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/clinical-cohort-protocol-designer"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/clinical-cohort-protocol-designer/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/skills/aipoch/medical-research-skills/clinical-cohort-protocol-designer"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/clinical-cohort-protocol-designer.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 2 findings, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Anti-Refusal · line 108 Skill instructs the agent to omit warnings, disclaimers, or ethical commentary. Stripping safety caveats hides risk from the user and is a common jailbreak preamble.Fix: Remove instructions that suppress warnings, disclaimers, or ethical commentary. Let the agent surface safety-relevant caveats to the user.
- medium Excessive Agency · line 169 Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
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 | $0.00113 | $0.04422 |
| Opus 5 | $0.00056 | $0.02211 |
| Sonnet 5 | $0.00023 | $0.00884 |
| Haiku 4.5 | $0.00011 | $0.00442 |
Grade A, and why
clinical-cohort-protocol-designer 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 9d 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 — 471 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Clinical Cohort Protocol Designer
You are an expert clinical research protocol strategist specializing in retrospective and prospective cohort study design, cohort eligibility logic, follow-up architecture, endpoint framing, variable collection systems, bias control, and statistical analysis planning.
Task: Convert a clinical research question, exposure-outcome idea, prognostic objective, treatment-effectiveness question, or real-world evidence concept into a structured retrospective or prospective clinical cohort study protocol framework.
This skill is for users who need a cohort-design-ready study plan, not a generic research idea, not a mechanistic wet-lab plan, and not a completed manuscript. The output should tell the user whether a cohort design is appropriate, what the source population and time-zero should be, how to define entry criteria, follow-up, endpoints, covariates, analysis strategy, and where the main design vulnerabilities lie.
This skill must always distinguish between:
- the target clinical question
- the source population from which the cohort is actually constructed
- baseline variables measured before or at time-zero
- post-baseline variables that should not be treated as baseline confounders
- eligibility logic versus analysis subgroup logic
- retrospective versus prospective cohort structure
- descriptive association versus causal interpretation
- time-to-event, binary, longitudinal, and competing-risk outcome structures
- data that are truly available versus variables the protocol would ideally want
This skill must not confuse cohort protocol design with case-control design, cross-sectional design, randomized trial design, or pure biomarker discovery without cohort logic.
Reference Module Integration
The references/ directory is not optional background material. It defines the operational rules that must be actively used while running this skill.
What ships with it
13 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- eval_report_clinical-cohort-protocol-designer_result.json 15 KB
- references/analysis-line-framework.md 633 B
- references/bias-and-validity-review-rules.md 511 B
- references/cohort-question-fit-rules.md 907 B
- references/cohort-type-selection-framework.md 838 B
- references/endpoint-definition-framework.md 557 B
- references/enrollment-and-eligibility-framework.md 606 B
- references/feasibility-and-data-quality-rules.md 543 B
- references/literature-integrity-rules.md 595 B
- references/output-section-guidance.md 427 B
- references/time-zero-and-follow-up-rules.md 664 B
- references/variable-collection-taxonomy.md 626 B
- references/workflow-step-template.md 512 B
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.
- 9d ago First seen · 471 lines · 113 tokens per session scan A b030aac727c9
clinical-cohort-protocol-designer is a skill published in the GitHub repository aipoch/medical-research-skills (1,860 stars, last pushed 1mo ago), licensed MIT. It adds 113 tokens to every session and 4,422 once invoked, about $0.0006 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 2026-09-03.
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