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Agent skill

Protocol To Executable JSON

by InternScience in InternScience/scp

Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.

MITAuto-check passed

Install Protocol To Executable JSON

skills CLI
$ npx skills add InternScience/scp --skill protocol-to-executable-json -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install InternScience/scp protocol-to-executable-json --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/protocol-to-executable-json .claude/skills/protocol-to-executable-json && rm -rf skills-src

Use ~/.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/

Facts

Skill name
protocol-to-executable-json
GitHub stars
169
Used in
1 other repo
Token cost
~718 tokens
SKILL.md length
49 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.

  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Protocol To Executable JSON is an agent skill from InternScience/scp. Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.

Its SKILL.md is about 720 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

The licence is MIT.

Example prompts

  • “/protocol-to-executable-json”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. 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

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

    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

Protocol To Executable JSON loads about 718 tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 49 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~34
When it runs · the whole SKILL.md, loaded when a task matches
~718

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 InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 49 words, ~718 tokens.

Download SKILL.mdSave it as .claude/skills/protocol-to-executable-json/SKILL.md (or your agent's skills folder).
name
protocol-to-executable-json
description
Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.
license
MIT license
metadata.skill-author
PJLab

Protocol to Executable JSON Conversion

Usage

python
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class ThothClient:
    def __init__(self, server_url: str):
        self.server_url = server_url
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(url=self.server_url, sse_read_timeout=60 * 10)
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            return False

    async def disconnect(self):
        if self.session:
            await self.session_ctx.__aexit__(None, None, None)
        if hasattr(self, 'transport'):
            await self.transport.__aexit__(None, None, None)

    def parse_result(self, result):
        try:
            if hasattr(result, 'content') and result.content:
                content = result.content[0]
                if hasattr(content, 'text'):
                    return json.loads(content.text)
            return str(result)
        except:
            try:
                return result.content[0].text
            except:
                return {"error": "parse error", "raw": str(result)}

## Initialize and use
client = ThothClient("https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan")
await client.connect()

# Protocol text
protocol = """
1. Prepare 5'/3' primer working stock by diluting each primer 1:10.
2. Set up PCR master mix according to the table.
3. Pipette 20 µL of PCR master mix into appropriate PCR tubes.
"""

# Convert to executable JSON
result = await client.session.call_tool("generate_executable_json", arguments={"protocol": protocol})
executable_json = client.parse_result(result)

# Execute the JSON
result = await client.session.call_tool("execute_json", arguments={"executable_json": json.dumps(executable_json)})
execution_info = client.parse_result(result)
print("Execution steps:")
print(execution_info)

await client.disconnect()
Tools:

  • generate_executable_json: Convert protocol text to executable JSON

    • Args: protocol (str) - Protocol text
    • Returns: JSON with executable steps

  • execute_json: Execute JSON protocol

    • Args: executable_json (str) - JSON string
    • Returns: Execution log with step-by-step operations
Use Cases
  • Lab automation, robotic liquid handling, protocol standardization, reproducibility

© InternScience, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/protocol-to-executable-json of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Protocol To Executable JSON 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.

Protocol To Executable JSON compared with similar skills
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Protocol Reversesickn33/agentic-awesome-skills47k1 repos~689Automated safety check: PassMIT
Protocol Reversezhaoxuya520/reverse-skill40k2 repos~620Automated safety check: WarnMIT

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Questions about Protocol To Executable JSON

What does Protocol To Executable JSON do?

Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control. Protocol To Executable JSON is an agent skill from InternScience/scp. Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.

How do I install Protocol To Executable JSON in Claude Code?

Run `npx skills add InternScience/scp --skill protocol-to-executable-json -a claude-code`. Or copy the skill folder (skills/protocol-to-executable-json in InternScience/scp) into .claude/skills/protocol-to-executable-json in your project. Claude Code loads it when a task matches its description.

How do I install Protocol To Executable JSON in Codex?

Run `npx skills add InternScience/scp --skill protocol-to-executable-json -a codex`. Or copy the skill folder (skills/protocol-to-executable-json in InternScience/scp) into .agents/skills/protocol-to-executable-json in your project. Codex loads it when a task matches its description.

Can I use Protocol To Executable JSON 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 InternScience/scp --skill protocol-to-executable-json -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/protocol-to-executable-json, .gemini/skills/protocol-to-executable-json, .github/skills/protocol-to-executable-json and .opencode/skills/protocol-to-executable-json in your project.

What does Protocol To Executable JSON need to run?

SKILL.md names no scripts, command-line tools or credentials: Protocol To Executable JSON is instructions for the agent only. Our summary lists: Python 3.

Does Protocol To Executable JSON 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 Protocol To Executable JSON 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 Protocol To Executable JSON use?

Protocol To Executable JSON 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 Protocol To Executable JSON use?

About 718 tokens (SKILL.md is roughly 2.9k 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 Protocol To Executable JSON?

Skills that share tags, products or a category with Protocol To Executable JSON: Convert (remotion-dev/remotion, 62k stars), Execute (alirezarezvani/claude-skills, 28k stars), Swift Protocol Di Testing (affaan-m/ECC, 274k stars) and Protocol Reverse (sickn33/agentic-awesome-skills, 47k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Protocol To Executable JSON?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.