MCP.science: Open Source MCP Servers for Scientific Research 🔍📚

by pathintegral-institute

142 stars

553 downloads

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GitHub Website

About

A collection of open-source MCP servers designed for scientific research applications.

Details

Author: pathintegral-institute
GitHub stars: 142
Downloads: 553
Categories: Other, Knowledge Base, Automation, Search

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 MCP.science: Open Source MCP Servers for Scientific Research 🔍📚

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": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

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": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

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": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

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": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

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": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

From the repository

Install the uv tool and an MCP-enabled client (e.g., Claude Desktop). Launch any server with uvx mcp-science <server-name>. Configure the command in your client’s settings (e.g., JSON config for Claude Desktop). A step-by-step guide is available in the repository.

Claude Desktop / Cursor

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

{
    "mcpServers": {
        "mcp.science: open source mcp servers for scientific research \ud83d\udd0d\ud83d\udcda": {
            "mcp.science": {
                "command": "uvx",
                "args": [
                    "mcp-science",
                    "web-fetch"
                ]
            }
        }
    }
}

McpServers

{
    "mcp.science": {
        "command": "uvx",
        "args": [
            "mcp-science",
            "web-fetch"
        ]
    }
}

MCP.science: Open Source MCP Servers for Scientific Research 🔍📚

_Join us in accelerating scientific discovery with AI and open-source tools!_

</div>

Quick Start

Running any server in this repository is as simple as a single command. For example, to start the web-fetch server:

uvx mcp-science web-fetch

This command handles everything from installation to execution. For more details on configuration and finding other servers, see the "How to configure MCP servers for AI client apps" section below.

- About
- What is MCP?
- Available servers in this repo
- How to integrate MCP servers into LLM
- How to build your own MCP server
- Contributing
- License
- Acknowledgments
- Citation

About

This repository contains a collection of open source MCP servers specifically designed for scientific research applications. These servers enable Al models (like Claude) to interact with scientific data, tools, and resources through a standardized protocol.

What is MCP?

> MCP is an open protocol that standardizes how applications provide context to LLMs. Think of MCP like a USB-C port for AI applications. Just as USB-C provides a standardized way to connect your devices to various peripherals and accessories, MCP provides a standardized way to connect AI models to different data sources and tools.
>
> MCP helps you build agents and complex workflows on top of LLMs. LLMs frequently need to integrate with data and tools, and MCP provides:
>
> - A growing list of pre-built integrations that your LLM can directly plug into
> - The flexibility to switch between LLM providers and vendors
> - Best practices for securing your data within your infrastructure
>
> Source: https://modelcontextprotocol.io/introduction

Available servers in this repo

Below is a complete list of the MCP servers that live in this monorepo. Every
entry links to the sub-directory that contains the server’s source code and
README so that you can find documentation and usage instructions quickly.

Example Server

An example MCP server that demonstrates the minimal pieces required for a server implementation.

Materials Project

A specialised MCP server that enables AI assistants to search, visualise and manipulate materials-science data from the Materials Project database. A Materials Project API key is required.

Python Code Execution

Runs Python code snippets in a secure, sandboxed environment with restricted standard-library access so that assistants can carry out analysis and computation without risking your system.

SSH Exec

Allows an assistant to run pre-validated commands on remote machines over SSH with configurable authentication and command whitelists.

Web Fetch

Fetches and processes HTML, PDF and plain-text content from the Web so that the assistant can quote or summarise it.

TXYZ Search

Performs Web, academic and “best effort” searches via the TXYZ API. A TXYZ API key is required.

Timer

A minimal countdown timer that streams progress updates to demonstrate MCP notifications.

GPAW Computation

Provides density-functional-theory (DFT) calculations through the GPAW package.

Jupyter-Act

Lets an assistant interact with a running Jupyter kernel, executing notebook cells programmatically.

Mathematica-Check

Evaluates small snippets of Wolfram Language code through a headless Mathematica instance.

NEMAD

Neuroscience Model Analysis Dashboard server that exposes tools for inspecting NEMAD data-sets.

TinyDB

Provides CRUD access to a lightweight JSON database backed by TinyDB so that an assistant can store and retrieve small pieces of structured data.

How to configure MCP servers for AI client apps

If you're not familiar with these stuff, here is a step-by-step guide for you: Step-by-step guide to configure MCP servers for AI client apps

Prerequisites

1. uv — a super-fast (Rust-powered) drop-in
replacement for pip + virtualenv. Install it with:

   curl -sSf https://astral.sh/uv/install.sh | bash

2. An MCP-enabled client application such as
Claude Desktop,
VSCode,
Goose,
5ire.

The short version – use `uvx`

Any server in this repository can be launched with a single shell command. The
pattern is:

uvx mcp-science <server-name>

For example, to start the web-fetch stdio server locally, configure the following command in your client:

uvx mcp-science web-fetch

Which corresponds to this in claude desktop's json configuration:

{

  "mcpServers": {

    "web-fetch": {

      "command": "uvx",

      "args": [

        "mcp-science",

        "web-fetch"

      ]

    }

  }

}

The command will download the mcp-science package from PyPI and run the requested entry-point.

Find other servers

Have a look at the Available servers list —
every entry in the table works with the pattern shown above.

---

Optional: managing integrations with MCPM

MCPM is a convenience command-line tool that can automate
the process of wiring servers into supported clients. It is not required but
can be useful if you frequently switch between clients or maintain a large
number of servers.

The basic workflow is:

```bash

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About

Details

Jump to

Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

MCP.science: Open Source MCP Servers for Scientific Research 🔍📚

Quick Start

Table of Contents

About

What is MCP?

Available servers in this repo

How to configure MCP servers for AI client apps

Prerequisites

The short version – use uvx

Find other servers

Optional: managing integrations with MCPM

Install

More like this

The short version – use `uvx`