Protocolsio Tools#

Configuration File: protocolsio_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the protocolsio_tools.json configuration file.

Available Tools#

ProtocolsIO_get_protocol (Type: ProtocolsIOTool)#

Get full detail for a specific protocols.io protocol by its numeric ID, URI slug, or DOI. Returns…

ProtocolsIO_get_protocol tool specification

Tool Information:

  • Name: ProtocolsIO_get_protocol

  • Type: ProtocolsIOTool

  • Description: Get full detail for a specific protocols.io protocol by its numeric ID, URI slug, or DOI. Returns title, description, materials/reagents list, ordered authors, DOI, and publication metadata. Requires PROTOCOLS_IO_API_KEY (OAuth Bearer token) environment variable. Use after ProtocolsIO_search_protocols to inspect a specific hit in full, or when the user already has a protocols.io ID/DOI.

Parameters:

  • operation (string) (optional) Operation type

  • protocol_id ([‘integer’, ‘string’]) (required) protocols.io protocol ID (integer), URI slug, or DOI (e.g., 65123, or ‘dx.doi.org/10.17504/protocols.io.xxxxx’).

  • content_format ([‘string’, ‘null’]) (optional) Format for free-text fields (description, steps). Default ‘json’.

Example Usage:

query = {
    "name": "ProtocolsIO_get_protocol",
    "arguments": {
        "protocol_id": "example_value"
    }
}
result = tu.run(query)

ProtocolsIO_get_protocol_steps (Type: ProtocolsIOTool)#

Get the ordered step-by-step instructions for a specific protocols.io protocol by its numeric ID,…

ProtocolsIO_get_protocol_steps tool specification

Tool Information:

  • Name: ProtocolsIO_get_protocol_steps

  • Type: ProtocolsIOTool

  • Description: Get the ordered step-by-step instructions for a specific protocols.io protocol by its numeric ID, URI slug, or DOI. Returns each step’s components (text, images, timers, reagents referenced) in sequence. Requires PROTOCOLS_IO_API_KEY (OAuth Bearer token) environment variable. Use once a specific protocol has been identified (via ProtocolsIO_search_protocols or ProtocolsIO_get_protocol) and the actual bench-level steps are needed.

Parameters:

  • operation (string) (optional) Operation type

  • protocol_id ([‘integer’, ‘string’]) (required) protocols.io protocol ID (integer), URI slug, or DOI.

  • content_format ([‘string’, ‘null’]) (optional) Format for step text. Default ‘json’.

Example Usage:

query = {
    "name": "ProtocolsIO_get_protocol_steps",
    "arguments": {
        "protocol_id": "example_value"
    }
}
result = tu.run(query)

ProtocolsIO_search_protocols (Type: ProtocolsIOTool)#

Search protocols.io’s public repository of peer-reviewed and community-submitted lab protocols by…

ProtocolsIO_search_protocols tool specification

Tool Information:

  • Name: ProtocolsIO_search_protocols

  • Type: ProtocolsIOTool

  • Description: Search protocols.io’s public repository of peer-reviewed and community-submitted lab protocols by keyword. Returns matching protocol titles, IDs, authors, and publication dates. protocols.io covers most wet-lab and computational method categories (molecular biology, cell culture, imaging, sequencing, etc.). Requires PROTOCOLS_IO_API_KEY (OAuth Bearer token) environment variable. Use for: finding a published step-by-step method before writing your own, checking how others perform a specific technique.

Parameters:

  • operation (string) (optional) Operation type

  • query (string) (required) Keyword(s) to search across protocol titles, descriptions, and authors (e.g., ‘CRISPR knockout’, ‘single cell RNA-seq library prep’).

  • order_field ([‘string’, ‘null’]) (optional) Sort field. Default ‘relevance’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 10, max 50).

Example Usage:

query = {
    "name": "ProtocolsIO_search_protocols",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)