BOLD MCP Server

by Lespernater

178 downloads

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MCP Server to connect local LLMs to BOLD Rest API

Details

Author: Lespernater
Downloads: 178
Categories: Other

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name BOLD MCP Server

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

From the repository

Install with pip from the cloned repository, then run python -m mcp_server_bold. Configure it as an MCP server in the Claude Desktop app by adding the command to claude_desktop_config.json. Use the tools specimen-search and combined-search to retrieve BOLD data.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "bold mcp server": {
            "bold": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_server_bold"
                ]
            }
        }
    }
}

McpServers

{
    "bold": {
        "command": "python",
        "args": [
            "-m",
            "mcp_server_bold"
        ]
    }
}

BOLD MCP Server

A Model Context Protocol server that provides capabilities for searching BOLD specimens. This server enables LLMs to retrieve and process content related to specific BOLD Rest API search queries in a simplified manner.

Available Tools

- specimen-search - Fetches specimen data based on given criteria.
- combined-search - Fetches specimen and sequence data based on given criteria.

Installation

Using PIP

You can install mcp-server-bold via pip:

git clone https://github.com/Lespernater/mcp-server-bold.git
cd mcp-server-bold
pip install -e .

After installation, you can run it as a script using:

python -m mcp_server_bold

You now can also run a locally hosted MCP interpreter for debugging using:

npx @modelcontextprotocol/inspector python -m mcp_server_bold

Configuration

Configure for Claude Destop App

Add to your claude_desktop_config.json, found easiest through the Claude Desktop settings:

<details>
<summary>Add to claude config:</summary>

"mcpServers": {
  "bold": {
    "command": "python",
    "args": ["-m", "mcp_server_bold"]
  }
}

</details>

You'll need to restart Claude Desktop, you should see a new plug icon and/or hammer icons in your chat prompt that confirms the BOLD MCP Server is detected.

Each time you create a new chat that queries BOLD through the MCP Server, you will have to agree to permit access to the MCP Server's Tool.

If it isn't working with the above set up, you can try creating a separate conda env and running Claude from there.

conda activate <custom_env>
git clone https://github.com/Lespernater/mcp-server-bold.git
cd mcp-server-bold
pip install -e .
open -a "Claude"

You may also need to point to absolute path of python in claude_desktop_config.json

<details>
<summary>Add to claude config:</summary>

"mcpServers": {
  "bold": {
    "command": "/path/to/bin/python",
    "args": ["-m", "mcp_server_bold"]
  }
}

</details>

Other hosts will be added as they become available (Zed currently doesn't support MCP Tools)

Debugging

You can use the MCP inspector to debug the server. If you've installed the package in a specific directory or are developing on it:

cd path/to/servers/src/mcp_server_bold
npx @modelcontextprotocol/inspector python -m mcp_server_bold

Contributing

We encourage contributions to help expand and improve mcp-server-bold. Whether you want to add new tools, enhance existing functionality, or improve documentation, your input is valuable.

For examples of other MCP servers and implementation patterns, see:
https://github.com/modelcontextprotocol/servers

Pull requests are welcome! Feel free to contribute new ideas, bug fixes, or enhancements to make mcp-server-bold even more powerful and useful.

License

mcp-server-bold is licensed under the MIT License. This means you are free to use, modify, and distribute the software, subject to the terms and conditions of the MIT License. For more details, please see the LICENSE file in the project repository.

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About

Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

BOLD MCP Server

Available Tools

Installation

Using PIP

Configuration

Configure for Claude Destop App

Other hosts will be added as they become available (Zed currently doesn't support MCP Tools)

Debugging

Contributing

License

Install

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