Research Refine
zjYao36/Auto-Research-Refine
Turns a vague research direction into a focused, problem-anchored method plan through up to five review rounds with a second model.
Official agent skill
Clinical Protocol Drafting
by aws-samples in aws-samples/amazon-bedrock-agents-healthcare-lifesciences
A skill your agent uses when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312).
Install Clinical Protocol Drafting
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-drafting --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/clinical-protocol-drafting .claude/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .claude/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-draftingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-drafting --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/clinical-protocol-drafting .agents/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .agents/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-drafting --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/clinical-protocol-drafting .cursor/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .cursor/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git --path skills/clinical-protocol-drafting--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-drafting --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/clinical-protocol-drafting .gemini/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .gemini/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-draftingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/clinical-protocol-drafting .github/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .github/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aws-samples/amazon-bedrock-agents-healthcare-lifesciences clinical-protocol-drafting --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/clinical-protocol-drafting .opencode/skills/clinical-protocol-drafting && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "clinical-protocol-drafting" agent skill from https://github.com/aws-samples/amazon-bedrock-agents-healthcare-lifesciences/tree/main/skills/clinical-protocol-drafting into .opencode/skills/clinical-protocol-drafting/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-protocol-drafting", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
clinical-protocol-drafting- GitHub stars
- 274
- Token cost
- ~1.4k tokens
- SKILL.md length
- 661 words
- Files
- 4 (incl. scripts, references)
- Skills in repo
- 12
- Repo updated
- First seen
- Licence
- MIT-0
At a glance
A skill your agent uses when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312).
- Works in 4 steps: Objectives Section → Background & Rationale Section → Study Design Section → …
- Drafting clinical trial protocol sections (objectives
- SKILL.md covers When to use this skill, MCP Dependencies, Workflow: Protocol Drafting… and Conventions, plus 1 more section
- Study design) grounded in ICH guidelines (E6
What it does
Clinical Protocol Drafting is an agent skill from aws-samples/amazon-bedrock-agents-healthcare-lifesciences, published by the product's own GitHub organization. Use when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312). Generates IRB-ready protocol documents from grant documents or study synopses.
Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `references/ich-knowledge-base-setup.md`).
It sits in Research & Science, covering Clinical and healthcare research and Experimental design. It works with Model Context Protocol. The licence is MIT-0.
When your agent uses it
- Drafting clinical trial protocol sections (objectives
- Study design) grounded in ICH guidelines (E6
- FDA regulations (21 CFR Part 312)
Example prompts
- “/clinical-protocol-drafting”
Workflow steps
4 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 9960565. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/, which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Clinical Protocol Drafting loads about 1.4k tokens when it runs, and up to ~2.4k if it reads all its reference files. Until then it costs about 69 tokens; SKILL.md has 661 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from aws-samples/amazon-bedrock-agents-healthcare-lifesciences at commit 9960565, republished under its MIT-0 licence (© aws-samples). 661 words, ~1,405 tokens.
Download SKILL.mdSave it as
.claude/skills/clinical-protocol-drafting/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- clinical-protocol-drafting
- description
- Use when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312). Generates IRB-ready protocol documents from grant documents or study synopses.
Clinical Trial Protocol Drafting
When to use this skill
- Draft protocol sections from a grant document or study synopsis
- Generate objectives, background/rationale, or study design sections
- Ensure protocol language complies with ICH E6(R2), E8(R1), E9
- Check regulatory requirements from 21 CFR Part 312 for IND protocols
- Assemble multiple sections into a cohesive protocol document
MCP Dependencies
| MCP Server | Tool | Purpose |
|---|---|---|
| fda-ecfr | get_cfr_section | Retrieve 21 CFR regulatory text |
| fda-ecfr | search_cfr | Search across CFR titles |
| awslabs.bedrock-kb-retrieval-mcp-server | retrieve | Query ICH E6/E8/E9 content via Bedrock Knowledge Base |
The fda-ecfr server is in mcp-servers/agentcore-gateway/fda-ecfr/ — deploy it first.
For ICH guidelines, set up a Bedrock Knowledge Base per references/ich-knowledge-base-setup.md and use the existing awslabs bedrock-kb-retrieval-mcp-server.
Workflow: Protocol Drafting from Grant Document
Step 1: Objectives Section
Generate the draft Objectives section of a clinical trial protocol.
- Extract from the grant: specific aims, primary endpoint, secondary endpoints.
- Use
retrievewith query "protocol objectives requirements ICH E6(R2) Section 6" to retrieve guidance on how protocol objectives should be stated.
Output structure:
- Primary Objective (linked to the primary endpoint)
- Secondary Objectives (linked to each secondary endpoint)
- Exploratory Objectives (if any are implied by the grant aims)
Each objective: clear, measurable, single-sentence statement following ICH conventions. Map each objective to its corresponding endpoint.
Step 2: Background & Rationale Section
Generate the draft Background and Rationale section.
- Extract from the grant: disease context, preliminary data (preclinical and Phase 1 results), unmet medical need, scientific rationale for the investigational agent.
- Use
get_cfr_sectionwith part "312" and section "23" to retrieve 21 CFR 312.23 requirements on nonclinical and clinical background information for an IND protocol. - Use
retrievewith query "protocol background section requirements ICH E6(R2) E8(R1)" to retrieve guidance.
Output structure:
- Disease Overview (epidemiology, molecular subtype prevalence, current standard of care)
- Unmet Medical Need (limitations of existing therapies)
- Investigational Agent Summary (mechanism of action, selectivity profile)
- Relevant Nonclinical Findings (IC50 data, selectivity over wild-type)
- Clinical Experience to Date (Phase 1 dose-escalation results, RP2D, preliminary efficacy and safety signals)
- Study Rationale (why this agent, this population, this design)
Tone: scientific, appropriate for IRB submission. Cite grant preliminary data where applicable.
Show full SKILL.md (312 more words)Show less
Step 3: Study Design Section
Generate the draft Study Design section.
- Extract from the grant: study design type, randomization scheme, treatment arms, dosing, sample size, study duration, number of sites, target population.
- Use
retrievewith query "general study design considerations randomization ICH E8(R1)" for design guidance. - Use
retrievewith query "statistical design principles sample size ICH E9" for statistical principles. - Use
get_cfr_sectionwith part "312" and section "23" for 21 CFR 312.23(a)(6) requirements on protocol design elements.
Output structure:
- Overall Design (phase, randomization ratio, open-label justification, multicenter)
- Treatment Arms (experimental arm with dose/schedule, control arm with regimen options)
- Study Schema (text-based visual flow: screening → randomization → treatment → follow-up)
- Randomization and Stratification (method, stratification factors if applicable)
- Sample Size Justification (statistical basis, power, expected effect size)
- Study Duration (enrollment period, treatment duration, follow-up period)
Step 4: Assembly
Assemble all drafted sections into a single cohesive protocol document.
Formatting:
- Protocol title page (study title, PI, funding source, protocol version/date)
- Sequential section numbering
- Consistent formatting, tense, and terminology
- Table of Contents
- Cross-reference harmonization (objectives referenced in study design)
- Flag inconsistencies as reviewer comments
Do not alter scientific content. Only harmonize language and ensure smooth transitions.
Conventions
- Lead with the most clinically relevant information in each section
- Use ICH-compliant terminology throughout (e.g., "investigational medicinal product" not "drug")
- Distinguish primary from secondary objectives clearly
- Include regulatory citations inline (e.g., "per 21 CFR 312.23(a)(6)")
- For VUS or uncertain data: note limitations and recommend additional review
- Never fabricate clinical data — use only what is provided in the source document
- Flag sections where the grant provides insufficient detail for protocol-level specificity
Regulatory References
- ICH E6(R2): Good Clinical Practice, Integrated Addendum
- ICH E8(R1): General Considerations for Clinical Studies
- ICH E9: Statistical Principles for Clinical Trials
- 21 CFR Part 312: Investigational New Drug Application
- 21 CFR Part 50: Protection of Human Subjects
- 21 CFR Part 56: Institutional Review Boards
© aws-samples, MIT-0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 3 other files (scripts, references) in skills/clinical-protocol-drafting of aws-samples/amazon-bedrock-agents-healthcare-lifesciences.
- SKILL.md
- references/.gitkeep
- references/ich-knowledge-base-setup.md
- scripts/.gitkeep
Open the folder on GitHubat commit 9960565
Compare with similar skills
Clinical Protocol Drafting next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Clinical Protocol Drafting this skillaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~1.4k | Automated safety check: Pass | MIT-0 | |
| Research RefinezjYao36/Auto-Research-Refine | 128 | 7 repos | ~6.9k | Automated safety check: Notes | None | |
| Medical Imaging ReviewLeonChaoX/qinyan-academic-skills | 937 | 3 repos | ~1.1k | Automated safety check: Notes | MIT | |
| Medical Research ToolkitFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.4k | Automated safety check: Pass | None | |
| Bgpt Paper Searchmajiayu000/claude-skill-registry | 666 | 4 repos | ~619 | Automated safety check: Notes | MIT | |
| Indication DossierJimLiu/science-skills | 227 | 4 repos | ~1.4k | Automated safety check: Pass | Apache-2.0 |
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Questions about Clinical Protocol Drafting
What does Clinical Protocol Drafting do?
A skill your agent uses when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312). Clinical Protocol Drafting is an agent skill from aws-samples/amazon-bedrock-agents-healthcare-lifesciences, published by the product's own GitHub organization. Use when drafting clinical trial protocol sections (objectives, background, study design) grounded in ICH guidelines (E6, E8, E9) and FDA regulations (21 CFR Part 312).
When should I use Clinical Protocol Drafting?
Clinical Protocol Drafting fits situations like: drafting clinical trial protocol sections (objectives; study design) grounded in ICH guidelines (E6; FDA regulations (21 CFR Part 312).
How do I install Clinical Protocol Drafting in Claude Code?
Run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a claude-code`. Or copy the skill folder (skills/clinical-protocol-drafting in aws-samples/amazon-bedrock-agents-healthcare-lifesciences) into .claude/skills/clinical-protocol-drafting in your project. Claude Code loads it when a task matches its description.
How do I install Clinical Protocol Drafting in Codex?
Run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a codex`. Or copy the skill folder (skills/clinical-protocol-drafting in aws-samples/amazon-bedrock-agents-healthcare-lifesciences) into .agents/skills/clinical-protocol-drafting in your project. Codex loads it when a task matches its description.
Can I use Clinical Protocol Drafting in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aws-samples/amazon-bedrock-agents-healthcare-lifesciences --skill clinical-protocol-drafting -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clinical-protocol-drafting, .gemini/skills/clinical-protocol-drafting, .github/skills/clinical-protocol-drafting and .opencode/skills/clinical-protocol-drafting in your project.
What does Clinical Protocol Drafting need to run?
SKILL.md names no scripts, command-line tools or credentials: Clinical Protocol Drafting is instructions for the agent only.
Does Clinical Protocol Drafting access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Clinical Protocol Drafting safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Clinical Protocol Drafting use?
Clinical Protocol Drafting is published under the MIT-0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Clinical Protocol Drafting use?
About 1.4k tokens (SKILL.md is roughly 5.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1k tokens, read only when the agent opens those files.
What are the alternatives to Clinical Protocol Drafting?
Skills that share tags, products or a category with Clinical Protocol Drafting: Research Refine (zjYao36/Auto-Research-Refine, 128 stars), Medical Imaging Review (LeonChaoX/qinyan-academic-skills, 937 stars), Medical Research Toolkit (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars) and Bgpt Paper Search (majiayu000/claude-skill-registry, 666 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Clinical Protocol Drafting?
aws-samples (a GitHub organization, an official publisher) maintains it in aws-samples/amazon-bedrock-agents-healthcare-lifesciences, which has 274 GitHub stars. The repository holds 12 skills in this directory. The repository was last updated on October 1, 2026.
Source: aws-samples/amazon-bedrock-agents-healthcare-lifesciences on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.