Biomodels Tools

Configuration File: biomodels_tools.json Tool Type: Local Tools Count: 5

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_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 for specific parameters within BioModels entries. Find models containing parameters matchi…

BioModels_search_parameters tool specification

Tool Information:

  • Name: BioModels_search_parameters

  • Type: BioModelsRESTTool

  • Description: Search for specific parameters within BioModels entries. Find models containing parameters matching your query (e.g., reaction rates, initial concentrations, kinetic constants). Returns models with parameter names, values, and units. Essential for finding models with specific parameter values or discovering parameter ranges across multiple models. Use this for comparative analysis or parameter estimation studies.

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).

Example Usage:

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

biomodels_search (Type: BioModelsRESTTool)

Search for computational biological models in the EBI BioModels database by keyword. Returns mode…

biomodels_search tool specification

Tool Information:

  • Name: biomodels_search

  • Type: BioModelsRESTTool

  • Description: Search for computational biological models in the EBI BioModels database by keyword. Returns models with identifiers, names, formats (typically SBML), and URLs. Use this to find systems biology models related to specific biological processes (e.g., ‘glycolysis’, ‘apoptosis’, ‘cell cycle’), diseases, or pathways. Find model IDs to use with other BioModels tools for detailed information and downloads.

Parameters:

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

  • limit (integer) (optional) Maximum number of results to return

Example Usage:

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