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protocolsio-integration

Manage scientific protocols and workspace assets via the protocols.io API v3.

21|2|Updated Dec 8, 2025
Search Tags:#workspace#api integration#file upload#discussion#protocols.io#protocol management#doi publishing
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill protocolsio-integration-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: protocolsio-integration
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/protocolsio-integration
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill protocolsio-integration-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill removes friction in working with protocols.io by giving you an API-driven playbook for finding, creating, updating, collaborating on, and exporting scientific protocols.

Core Features & Use Cases

  • Protocol discovery and lifecycle management: Search by keywords/filters/DOI, retrieve full protocol details, create, update, and publish (including DOI issuance).
  • Step, materials, and publication control: Add, edit, delete, and reorder steps; manage reagents/materials; generate PDFs and handle content formats.
  • Collaboration and organization: Manage protocol and step discussions with threaded comments; organize content in workspaces with role-based permissions.
  • File and experiment operations: Upload/download and organize files; track protocol runs with experiment records; handle notifications and exports.

Quick Start

Use the skill to plan an end-to-end workflow with protocols.io API v3 by asking: "How do I search for a protocol by keyword, retrieve its steps, post a step-level comment, upload related files to the workspace, and then generate a PDF for sharing?"

Frequently Asked Questions about protocolsio-integration

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

FAQPage Schema
How do I search for a scientific protocol by keyword and retrieve its steps?▼

Protocol discovery is handled through the protocols.io API v3, letting you search by keywords, filters, or DOI to retrieve full protocol details including steps and materials.

Can I publish a scientific protocol and generate a DOI?▼

Yes, protocol lifecycle management supports publishing protocols directly, which includes DOI issuance for citation and generating PDFs for sharing.

Does protocols.io API integration support threaded discussions on specific protocol steps?▼

Threaded discussions are supported, enabling you to post and manage step-level comments and protocol-level collaboration directly through the API endpoints.

Do I need a Bearer token to upload files to a protocols.io workspace?▼

Yes, Bearer token authentication is required for all API v3 operations, including uploading, downloading, and organizing files within role-based permission workspaces.

What is the best way to manage scientific protocol experiments and notifications?▼

Experiment records and notification workflows are managed through dedicated API endpoints, enabling you to track protocol runs and handle automated alerts for updates.

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