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pradyumnasagar
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protocolsio-protocol-repository

Search protocols.io by keyword or DOI and extract protocol details.

6|2|Updated Jun 11, 2026
Search Tags:#data extraction#lab automation#protocols.io#protocol search#ELN integration
One-click install
npx skills add https://github.com/pradyumnasagar/open-research-skills --skill protocolsio-protocol-repository
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: protocolsio-protocol-repository
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/lab-automation/protocolsio-protocol-repository
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill protocolsio-protocol-repository

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, and includes scripts (resource) components.

What problem does it solve?

This Skill simplifies the process of finding and integrating wet-lab protocols from the protocols.io database, streamlining experimental workflows and enhancing reproducibility.

Core Features & Use Cases

  • Protocol Discovery: Search and download protocols by keyword, DOI, or filter.
  • Data Extraction: Extract steps, reagents, materials, timing, and equipment.
  • Automation: Use with opentrons-protocol-api for script generation.
  • ELN Integration: Record runs in an ELN system.
  • Use Case: When you need a specific protocol for a new experiment, this Skill can quickly locate the protocol, extract the necessary information, and integrate it into your lab automation system.

Quick Start

Use the 'protocolsio-protocol-repository' skill to search for "RNA extraction" protocols and retrieve details for the top 5 results.

Frequently Asked Questions about protocolsio-protocol-repository

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I extract wet-lab protocols from protocols.io for lab automation?▼

This Skill searches and retrieves wet-lab protocols from protocols.io by keyword or DOI, extracting structured data like steps, reagents, and equipment for lab automation workflows.

What is the best way to find a specific protocol by DOI for ELN integration?▼

The best way to find a specific protocol by DOI for ELN integration is to use this Skill's DOI lookup feature, which retrieves full protocol details and structured data for direct recording into your Electronic Lab Notebook.

Do I need Python and the requests library to search protocols.io?▼

Yes, you need Python and the requests library to run this Skill, as it relies on these dependencies to query the protocols.io database and return structured protocol data using pandas.

Can I use extracted protocols.io data with opentrons-protocol-api for script generation?▼

Yes, you can use the extracted protocols.io data with opentrons-protocol-api, because this Skill structures reagents, materials, and equipment outputs specifically to streamline lab automation script generation.

What limitations should I expect when doing a protocol search on protocols.io?▼

Limitations of this protocol search approach include dependency on the protocols.io API availability and the need for Python environments with requests and pandas, restricting use for non-technical lab users.

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