Biomodels Tools#

Configuration File: biomodels_tools.json Tool Type: Local Tools Count: 6

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

Available Tools#

BioModels_download_model (Type: BioModelsRESTTool)#

Download a specific file from a BioModels entry or get the download URL for the entire model as a…

BioModels_download_model tool specification

Tool Information:

  • Name: BioModels_download_model

  • Type: BioModelsRESTTool

  • Description: Download a specific file from a BioModels entry or get the download URL for the entire model as a COMBINE archive. Returns download URL and file metadata. Use this to access model files for simulation software (COPASI, CellDesigner, etc.). Specify filename parameter to download a specific file, or omit to get the COMBINE archive containing all files. Find model IDs using biomodels_search.

Parameters:

  • model_id (string) (required) BioModels identifier (e.g., ‘BIOMD0000000469’). Find IDs using biomodels_search.

  • filename (string) (optional) Optional specific filename to download. If not provided, returns COMBINE archive with all files. Use BioModels_list_files to see available filenames.

Example Usage:

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

BioModels_get_model (Type: BioModelsRESTTool)#

Get comprehensive metadata for a specific BioModels entry by its model identifier. Returns detail…

BioModels_get_model tool specification

Tool Information:

  • Name: BioModels_get_model

  • Type: BioModelsRESTTool

  • Description: Get comprehensive metadata for a specific BioModels entry by its model identifier. Returns detailed information including model name, description, publication references, organism, biological processes, SBML level/version, creation/modification dates, and curator annotations. Use this to understand model details, citations, and biological context before downloading or using a model. Find model IDs using biomodels_search (e.g., ‘BIOMD0000000469’, ‘MODEL1707110000’).

Parameters:

  • model_id (string) (required) BioModels identifier (e.g., ‘BIOMD0000000469’, ‘MODEL1707110000’). Find IDs using biomodels_search. Optionally append ‘.N’ for a specific revision (e.g., ‘BIOMD0000000469.1’).

Example Usage:

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

BioModels_list_all_model_ids (Type: BioModelsRESTTool)#

Enumerate ALL BioModels model identifiers - the complete registry of curated (BIOMD…) and non-c…

BioModels_list_all_model_ids tool specification

Tool Information:

  • Name: BioModels_list_all_model_ids

  • Type: BioModelsRESTTool

  • Description: Enumerate ALL BioModels model identifiers - the complete registry of curated (BIOMD…) and non-curated (MODEL…) model IDs. Unlike biomodels_search (keyword search) or BioModels_search_parameters, this returns the full catalog of model IDs so you can iterate over every model in BioModels. Returns a ‘hits’ count and a ‘models’ array of identifier strings (e.g. ‘BIOMD0000000001’). Use the returned IDs with BioModels_get_model, BioModels_list_files, or BioModels_download_model. The full registry currently contains ~3190 model identifiers.

Parameters:

No parameters required.

Example Usage:

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

BioModels_list_files (Type: BioModelsRESTTool)#

Get detailed file listing for a specific BioModels entry including file names, types, sizes, and …

BioModels_list_files tool specification

Tool Information:

  • Name: BioModels_list_files

  • Type: BioModelsRESTTool

  • Description: Get detailed file listing for a specific BioModels entry including file names, types, sizes, and metadata. Returns information about all files associated with the model (SBML files, figures, supplementary data, COMBINE archives). Use this before downloading to see what files are available and their formats. Requires model ID from biomodels_search or BioModels_get_model.

Parameters:

  • model_id (string) (required) BioModels identifier (e.g., ‘BIOMD0000000469’). Find IDs using biomodels_search.

Example Usage:

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

BioModels_search_parameters (Type: BioModelsRESTTool)#

Search parameters within BioModels entries using the parameter service’s size/start pagination. C…

BioModels_search_parameters tool specification

Tool Information:

  • Name: BioModels_search_parameters

  • Type: BioModelsRESTTool

  • Description: Search parameters within BioModels entries using the parameter service’s size/start pagination. Continue with metadata.next_offset while metadata.has_more is true; metadata.total_results is the exact filtered count. BioModels enforces a minimum upstream batch of 10, but this wrapper returns exactly the requested limit.

Parameters:

  • query (string) (required) Search query for parameters (e.g., parameter name like ‘k1’, ‘Km’, or biological term). Search across parameter names, values, and annotations.

  • limit (integer) (optional) Maximum number of results to return (default: 10, max: 100).

  • offset (integer) (optional) Zero-based parameter-record offset. Continue with metadata.next_offset.

Example Usage:

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

biomodels_search (Type: BioModelsRESTTool)#

Search EBI BioModels by keyword with recoverable offset pagination. Continue with metadata.next_o…

biomodels_search tool specification

Tool Information:

  • Name: biomodels_search

  • Type: BioModelsRESTTool

  • Description: Search EBI BioModels by keyword with recoverable offset pagination. Continue with metadata.next_offset while metadata.has_more is true; metadata.total_results is the exact upstream match count. BioModels enforces a minimum upstream batch of 10, but this wrapper returns exactly the requested limit.

Parameters:

  • query (string) (required) Search query for biological models

  • limit (integer) (optional) Maximum models to return on this page (1-100).

  • offset (integer) (optional) Zero-based model offset. Continue with metadata.next_offset.

Example Usage:

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