Protocols.io is a comprehensive platform for developing, sharing, and managing scientific protocols. This skill provides complete integration with the protocols.io API v3, enabling programmatic access to protocols, workspaces, discussions, file management, and collaboration features.
Fetches protocolsio-integration from davila7/claude-code-templates and configures it for Cursor.
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Protocols.io is a comprehensive platform for developing, sharing, and managing scientific protocols. This skill provides complete integration with the protocols.io API v3, enabling programmatic access to protocols, workspaces, discussions, file management, and collaboration features.
When to Use This Skill
Use this skill when working with protocols.io in any of the following scenarios:
Protocol Discovery: Searching for existing protocols by keywords, DOI, or category
Protocol Management: Creating, updating, or publishing scientific protocols
Step Management: Adding, editing, or organizing protocol steps and procedures
Collaborative Development: Working with team members on shared protocols
Workspace Organization: Managing lab or institutional protocol repositories
Discussion & Feedback: Adding or responding to protocol comments
File Management: Uploading data files, images, or documents to protocols
Experiment Tracking: Documenting protocol executions and results
Data Export: Backing up or migrating protocol collections
Integration Projects: Building tools that interact with protocols.io
Core Capabilities
This skill provides comprehensive guidance across five major capability areas:
1. Authentication & Access
Manage API authentication using access tokens and OAuth flows. Includes both client access tokens (for personal content) and OAuth tokens (for multi-user applications).
Key operations:
Generate authorization links for OAuth flow
Exchange authorization codes for access tokens
Refresh expired tokens
Manage rate limits and permissions
Reference: Read references/authentication.md for detailed authentication procedures, OAuth implementation, and security best practices.
2. Protocol Operations
Complete protocol lifecycle management from creation to publication.
Key operations:
Search and discover protocols by keywords, filters, or DOI
Retrieve detailed protocol information with all steps
Reference: Read references/protocols_api.md for comprehensive protocol management guidance, including API endpoints, parameters, common workflows, and examples.
3. Discussions & Collaboration
Enable community engagement through comments and discussions.
Key operations:
View protocol-level and step-level comments
Create new comments and threaded replies
Edit or delete your own comments
Analyze discussion patterns and feedback
Respond to user questions and issues
Reference: Read references/discussions.md for discussion management, comment threading, and collaboration workflows.
4. Workspace Management
Organize protocols within team workspaces with role-based permissions.
Key operations:
List and access user workspaces
Retrieve workspace details and member lists
Request access or join workspaces
List workspace-specific protocols
Create protocols within workspaces
Manage workspace permissions and collaboration
Reference: Read references/workspaces.md for workspace organization, permission management, and team collaboration patterns.
5. File Operations
Upload, organize, and manage files associated with protocols.
Key operations:
Search workspace files and folders
Upload files with metadata and tags
Download files and verify uploads
Organize files into folder hierarchies
Update file metadata
Delete and restore files
Manage storage and organization
Reference: Read references/file_manager.md for file upload procedures, organization strategies, and storage management.
6. Additional Features
Supplementary functionality including profiles, notifications, and exports.
Key operations:
Manage user profiles and settings
Query recently published protocols
Create and track experiment records
Receive and manage notifications
Export organization data for archival
Reference: Read references/additional_features.md for profile management, publication discovery, experiment tracking, and data export.
Getting Started
Step 1: Authentication Setup
Before using any protocols.io API functionality:
Obtain an access token (CLIENT_ACCESS_TOKEN or OAUTH_ACCESS_TOKEN)
Read references/authentication.md for detailed authentication procedures
Store the token securely
Include in all requests as: Authorization: Bearer YOUR_TOKEN
Step 2: Identify Your Use Case
Determine which capability area addresses your needs:
Working with protocols? → Read references/protocols_api.md
Managing team protocols? → Read references/workspaces.md
›Access to product documentation and roadmap tools (Jira, Notion, etc.)
›Understanding of product management frameworks (RICE, Jobs-to-be-Done, etc.)
›Stakeholder contact information and communication channels
Time Estimate
30-60 minutes to see productivity improvements
Steps
1Install product management skill
2Start with user story generation for known feature
3Progress to competitive analysis: research 2-3 competitors
4Use for roadmap prioritization: apply RICE/ICE scoring
5Draft stakeholder communications and refine based on feedback
6Build template library for recurring PM tasks
7Share effective prompts with product team
Common Pitfalls
⚠Not validating competitive research—verify facts before sharing
⚠Accepting user stories without involving engineering team
⚠Over-relying on frameworks without qualitative judgment
⚠Not customizing outputs to company culture and communication style
⚠Skipping stakeholder validation of generated requirements
Best Practices
✓ Do
+Validate research and competitive analysis with real data
+Collaborate with engineering when generating technical requirements
+Customize frameworks and templates to your company context
+Use skill for first drafts, refine with stakeholder input
+Document successful prompt patterns for PM tasks
+Combine AI efficiency with human judgment and intuition
✗ Don't
−Don't publish competitive analysis without fact-checking
−Don't finalize user stories without engineering review
−Don't make prioritization decisions solely on AI scoring
−Don't skip customer validation of generated requirements
−Don't ignore company-specific context and culture
💡 Pro Tips
★Provide context: company goals, constraints, customer feedback
★Ask for alternatives: 'Show 3 ways to prioritize this roadmap'
★Request stakeholder-specific formatting: 'Executive summary vs. engineering spec'
★Use skill for 70% generation + 30% customization to company needs
When to Use This
✓ Use when
Use for user story writing, competitive research, roadmap prioritization, stakeholder communication, and PRD drafting. Best for reducing repetitive documentation and research work.
✗ Avoid when
Avoid for strategic product vision (requires deep customer empathy), pricing decisions (needs market and financial expertise), or when face-to-face customer discovery is more valuable than speed.
Learning Path
1Basic: user stories, feature specs, status updates
