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Search, browse, and retrieve scientific protocols from protocols.io via REST API.
Install Protocols Io
$ npx skills add ClawBio/ClawBio --skill protocols-io -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ClawBio/ClawBio protocols-io --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/protocols-io .claude/skills/protocols-io && 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 "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .claude/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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/ClawBio/ClawBio/tree/main/skills/protocols-ioType 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 ClawBio/ClawBio --skill protocols-io -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ClawBio/ClawBio protocols-io --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/protocols-io .agents/skills/protocols-io && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .agents/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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 ClawBio/ClawBio --skill protocols-io -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ClawBio/ClawBio protocols-io --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/protocols-io .cursor/skills/protocols-io && 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 "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .cursor/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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/ClawBio/ClawBio.git --path skills/protocols-io--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 ClawBio/ClawBio --skill protocols-io -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ClawBio/ClawBio protocols-io --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/protocols-io .gemini/skills/protocols-io && 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 "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .gemini/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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 ClawBio/ClawBio protocols-ioInstalls 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 ClawBio/ClawBio --skill protocols-io -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/protocols-io .github/skills/protocols-io && 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 "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .github/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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 ClawBio/ClawBio --skill protocols-io -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ClawBio/ClawBio protocols-io --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/protocols-io .opencode/skills/protocols-io && 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 "protocols-io" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/protocols-io into .opencode/skills/protocols-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocols-io", 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
protocols-io- GitHub stars
- 1.2k
- Token cost
- ~1.9k tokens
- SKILL.md length
- 648 words
- Files
- 5
- Skills in repo
- 99
- Repo updated
- First seen
- Licence
- MIT
At a glance
Search, browse, and retrieve scientific protocols from protocols.io via REST API.
- Works in 5 steps: Client token authentication — Set your… → Protocol search — Search public (and… → Protocol retrieval — Fetch full protocol… → …
- User mentions protocols.io
- SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Workflow, plus 10 more sections
- Runs Python scripts from its folder; calls python; needs PROTOCOLS_IO_ACCESS_TOKEN
What it does
Protocols Io is an agent skill from ClawBio/ClawBio. Search, browse, and retrieve scientific protocols from protocols.io via REST API. Client token authentication for private protocols. Use when user mentions protocols.io, lab protocols, DOI lookup, protocol search, protocol steps, or scientific methods.
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files (for example `demo/demo_protocol.json`, `demo/demo_search_results.json` and `protocols_io.py`).
It sits in Backend & APIs, covering REST APIs and Authentication. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.
When your agent uses it
- User mentions protocols.io
- Protocol search
- Scientific methods
Example prompts
- “/protocols-io”
Requirements
- Python 3
- A credential in PROTOCOLS_IO_ACCESS_TOKEN
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Client token authentication — Set your access token from protocols.io/developers as PROTOCOLS_IO_ACCESS_TOKEN
- Protocol search — Search public (and private, when authenticated) protocols by keyword with pagination and sorting
- Protocol retrieval — Fetch full protocol details including steps, reagents, materials, authors, and DOI
- Step extraction — Retrieve protocol steps in markdown format for immediate use
- Demo mode — Pre-cached search results for offline demonstration
What it can do on your machine
Read from SKILL.md and the folder at commit cea08d1. 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 script files (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
protocols.ioapidocs.protocols.io
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
PROTOCOLS_IO_ACCESS_TOKEN
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Protocols Io loads about 1.9k tokens when it runs. Until then it costs about 66 tokens; SKILL.md has 648 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); files beside SKILL.md are not scanned.
SKILL.md
The full file from ClawBio/ClawBio at commit cea08d1, republished under its MIT licence (© ClawBio). 648 words, ~1,885 tokens.
Download SKILL.mdSave it as
.claude/skills/protocols-io/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.- name
- protocols-io
- description
- Search, browse, and retrieve scientific protocols from protocols.io via REST API. Client token authentication for private protocols. Use when user mentions protocols.io, lab protocols, DOI lookup, protocol search, protocol steps, or scientific methods.
- license
- MIT
- metadata.version
- 0.2.0
- metadata.author
- ClawBio Contributors
- metadata.tags
- protocols, lab-methods, reproducibility, protocols-io, scientific-methods, DOI
🧪 Protocols.io Bridge
You are Protocols.io Bridge, a specialised ClawBio agent for discovering and retrieving scientific protocols from protocols.io. Your role is to search, browse, and fetch full protocol details — including steps, reagents, and metadata — via the protocols.io REST API.
Why This Exists
- Without it: Users must manually browse protocols.io, copy-paste steps, and cannot programmatically access their private protocols
- With it: Search 200,000+ published protocols by keyword, retrieve full step-by-step methods, and access private/shared protocols — all from the CLI
- Why ClawBio: Grounded in the real protocols.io API v3/v4; protocols have DOIs and version history for reproducibility
Core Capabilities
- Client token authentication — Set your access token from protocols.io/developers as
PROTOCOLS_IO_ACCESS_TOKEN - Protocol search — Search public (and private, when authenticated) protocols by keyword with pagination and sorting
- Protocol retrieval — Fetch full protocol details including steps, reagents, materials, authors, and DOI
- Step extraction — Retrieve protocol steps in markdown format for immediate use
- Demo mode — Pre-cached search results for offline demonstration
Input Formats
| Format | Extension | Required Fields | Example |
|---|---|---|---|
| Search query | CLI arg | --search <keywords> | --search "RNA extraction" |
| Protocol ID | CLI arg | --protocol <id_or_uri> | --protocol 30756 |
| DOI | CLI arg | --protocol <doi> | --protocol "10.17504/protocols.io.baaciaaw" |
Workflow
When the user asks about scientific protocols or protocols.io:
- Authenticate (if needed): Read
PROTOCOLS_IO_ACCESS_TOKEN; if absent or expired, ask the user for one - Search/Retrieve: Execute the requested operation against the protocols.io API
- Format: Render results as a markdown report with protocol metadata, steps, and reagents
- Output: Print to terminal as markdown
CLI Reference
# Authenticate: export PROTOCOLS_IO_ACCESS_TOKEN first (see Authentication)
# Search protocols by keyword
python skills/protocols-io/protocols_io.py --search "CRISPR gene editing"
# Search with filters
python skills/protocols-io/protocols_io.py --search "RNA extraction" --peer-reviewed
python skills/protocols-io/protocols_io.py --search "RNA extraction" --published-on 2022-01-01
python skills/protocols-io/protocols_io.py --search "RNA extraction" --page-size 20 --page 2
python skills/protocols-io/protocols_io.py --search "RNA extraction" --filter user_private
# Retrieve a protocol by ID, URI, or DOI
python skills/protocols-io/protocols_io.py --protocol 30756
# Download protocol as PDF (saved to output dir)
python skills/protocols-io/protocols_io.py --protocol 30756 --output /tmp/protocols_io
# Get protocol steps only
python skills/protocols-io/protocols_io.py --steps 30756
# Demo mode (offline, pre-cached)
python skills/protocols-io/protocols_io.py --demo
# Via ClawBio runner
python clawbio.py run protocols-io --demo
python clawbio.py run protocols-io --search "RNA extraction"Authentication
- Go to protocols.io/developers
- Log in, find Your Applications, and copy your Access Token
export PROTOCOLS_IO_ACCESS_TOKEN=<token>(nothing is saved to disk)
Without the variable, --search, --protocol and --steps exit with an error naming it.
Demo
python skills/protocols-io/protocols_io.py --demoExpected output: a search results report for "RNA extraction" with 5 pre-cached protocol summaries, plus full detail for one protocol including steps and reagents.
Algorithm / Methodology
- Token management: Read
PROTOCOLS_IO_ACCESS_TOKEN; if expired (status 1219), ask the user for a new token - Search:
GET /api/v3/protocols?filter=public&key=<query>&order_field=relevance&page_size=10— parse paginated results - Retrieve:
GET /api/v4/protocols/<id>?content_format=markdown— returns full protocol with steps rendered as markdown - Steps:
GET /api/v4/protocols/<id>/steps?content_format=markdown— returns ordered step list
Rate limits: 100 requests/minute per user; over the limit the API returns HTTP 429. This client applies a sliding-window throttle and retries on 429 using Retry-After (capped, up to 3 retries). The /view/[protocol-uri].pdf endpoint is stricter (5/min signed-in, 3/min signed-out by IP); use --output (PDF download) with care.
Show full SKILL.md (244 more words)Show less
Example Queries
- "Search protocols.io for RNA extraction protocols"
- "Show me the steps for protocol 30756"
- "Find CRISPR protocols on protocols.io"
- "Get the protocol with DOI 10.17504/protocols.io.baaciaaw"
- "Log in to protocols.io to access my private protocols"
Output Structure
Without --output: results are printed to the terminal as markdown. With --output <dir>: all modes save report.md as the primary output; --protocol also downloads a PDF named after the protocol title. All modes write a reproducibility/ bundle (commands.sh, checksums.sha256, environment.yml).
Dependencies
Required (core dependency in pyproject.toml):
requests>= 2.28 — HTTP client for API calls
Optional:
- A protocols.io developer account for private protocol access (public search works without it)
Safety
- Local-first: Token is read from the environment and never written to disk; no data uploaded
- Disclaimer: Every report includes the ClawBio medical disclaimer
- No credential leakage: Client secret and tokens never appear in reports or logs
- Read-only by default: The skill only reads protocols; no create/edit/delete operations
- Rate-limit aware: Client-side 100 req/min sliding window; automatic back-off on HTTP 429
Integration with Bio Orchestrator
Trigger conditions — the orchestrator routes here when:
- User mentions "protocols.io", "protocol search", "lab protocol", "scientific protocol", "DOI lookup"
- User provides a protocols.io URL or DOI
Chaining partners:
lit-synthesizer: Cross-reference protocol citations with PubMed literaturelabstep: Import protocols.io methods into Labstep experimentsrepro-enforcer: Verify reproducibility of protocols.io methods
Citations
- protocols.io — Open access repository for scientific methods
- protocols.io API v3 Documentation — REST API reference
- Teytelman et al. (2016) "protocols.io: Virtual Communities for Protocol Development and Discussion" PLOS Biology
© ClawBio, MIT. 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 4 other files in skills/protocols-io of ClawBio/ClawBio.
- SKILL.md
- demo/demo_protocol.json
- demo/demo_search_results.json
- protocols_io.py
- tests/test_protocols_io.py
Open the folder on GitHubat commit cea08d1
Compare with similar skills
Protocols Io 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 |
|---|---|---|---|---|---|---|
| Protocols Io this skillClawBio/ClawBio | 1.2k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Laravel SpecialistJeffallan/claude-skills | 12k | 1 repos | ~2.1k | Automated safety check: Pass | MIT | |
| API Patternsdilolabs/nosia | 213 | 1 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Verify Authendpointsmadeyoga/AuthEndpoints | 121 | — | ~2.6k | Automated safety check: Pass | MIT | |
| Nodejs Express Serverever-works/ever-works | 158 | — | ~965 | Automated safety check: Pass | AGPL-3.0 | |
| API Debuggingownpilot/OwnPilot | 426 | — | ~824 | Automated safety check: Pass | MIT |
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Categories
Questions about Protocols Io
What does Protocols Io do?
Search, browse, and retrieve scientific protocols from protocols.io via REST API. Protocols Io is an agent skill from ClawBio/ClawBio.io via REST API.
When should I use Protocols Io?
Protocols Io fits situations like: user mentions protocols.io; protocol search; scientific methods.
How do I install Protocols Io in Claude Code?
Run `npx skills add ClawBio/ClawBio --skill protocols-io -a claude-code`. Or copy the skill folder (skills/protocols-io in ClawBio/ClawBio) into .claude/skills/protocols-io in your project. Claude Code loads it when a task matches its description.
How do I install Protocols Io in Codex?
Run `npx skills add ClawBio/ClawBio --skill protocols-io -a codex`. Or copy the skill folder (skills/protocols-io in ClawBio/ClawBio) into .agents/skills/protocols-io in your project. Codex loads it when a task matches its description.
Can I use Protocols Io 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 ClawBio/ClawBio --skill protocols-io -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/protocols-io, .gemini/skills/protocols-io, .github/skills/protocols-io and .opencode/skills/protocols-io in your project.
What does Protocols Io need to run?
Going by SKILL.md and its folder, Protocols Io needs Python for the scripts in its folder, the command-line tools its instructions call (python) and credentials named PROTOCOLS_IO_ACCESS_TOKEN. Our summary lists: Python 3; A credential in PROTOCOLS_IO_ACCESS_TOKEN.
Does Protocols Io access the network?
SKILL.md names 2 domains. As links in the text: protocols.io and apidocs.protocols.io. This is read from the text; nothing was executed.
Is Protocols Io 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. Review the folder before installing.
What licence does Protocols Io use?
Protocols Io is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Protocols Io use?
About 1.9k tokens (SKILL.md is roughly 7.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Protocols Io?
Skills that share tags, products or a category with Protocols Io: Laravel Specialist (Jeffallan/claude-skills, 12k stars), API Patterns (dilolabs/nosia, 213 stars), Verify Authendpoints (madeyoga/AuthEndpoints, 121 stars) and Nodejs Express Server (ever-works/ever-works, 158 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Protocols Io?
ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,152 GitHub stars. The repository holds 99 skills in this directory. The repository was last updated on October 6, 2026.
Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.