Atlas / MCP servers / pathintegral-institute / MCP.science: Open Source MCP Servers for Scientific Research

MCP.science: Open Source MCP Servers for Scientific ResearchCAUTION

Name: MCP.science: Open Source MCP Servers for Scientific Research
Author: pathintegral-institute

mcp/pathintegral-institute/mcp-science

MCP server by pathintegral-institute · Audited 2026-10-07

⚑ Report / re-scan Source ↗

Open Source MCP Servers for Scientific Research

Verdict

CAUTION

Grade

Trust score

86 /100

Exposed tools

42 24r · 14w · 4d

Transport

stdio · streamable-http

License

MIT

Stars

152

Overview

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

[](https://opensource.org/licenses/MIT)

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

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 pro

Read from source at commit 7168561a9c98OBSERVED · 2026-10-07

Connect

Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control. Replace the environment placeholders with a token scoped to the least it needs.

claude-code

claude mcp add web-fetch --env JINA_API_KEY=${JINA_API_KEY} --env JUPYTER_SERVER_TOKEN=${JUPYTER_SERVER_TOKEN} --env MP_API_KEY=${MP_API_KEY} --env NEMAD_API_KEY=${NEMAD_API_KEY} -- uvx web-fetch

claude-desktop

{
  "mcpServers": {
    "web-fetch": {
      "command": "uvx",
      "args": [
        "web-fetch"
      ],
      "env": {
        "JINA_API_KEY": "${JINA_API_KEY}",
        "JUPYTER_SERVER_TOKEN": "${JUPYTER_SERVER_TOKEN}",
        "MP_API_KEY": "${MP_API_KEY}",
        "NEMAD_API_KEY": "${NEMAD_API_KEY}"
      }
    }
  }
}

Exposed tools (42)

24 read · 14 write · 4 destructive. Blast radius: 4 tools can delete or overwrite — an agent that can be talked into calling a tool can be talked into calling this one.

Tool	Risk	Description
`add`	write	Add two numbers.
`analyze_eigenstate`	read	Analyze a specific eigenstate of a quantum system.
`analyze_ground_state`	read	Analyze the ground state properties of a quantum system.
`build_supercell`	read
`check_calculation_result`	read
`compute_energy_spectrum`	read	Compute the energy spectrum of a quantum system.
`create_new_project`	write
`create_quantum_system`	write	Create a new quantum system for analysis.
`create_structure_from_cif`	write
`create_structure_from_poscar`	write
`create_table`	write	Creates a new table in the database.
`delete_documents`	destructive	Deletes documents from the specified table.
`delete_quantum_system`	destructive	Delete a quantum system and its associated data.
`display_numerical_result`	read	Displays a saved plot for a given quantum system analysis.
`drop_table`	destructive	Drops the specified table from the database.
`execute_mathematica`	write
`generate_plot`	read	Generate plots for quantum system analysis.
`get_image_of_flower`	read	Get an image of flower
`get_system_details`	read	Get detailed information about a specific quantum system.
`insert_document`	write	Inserts a document into the specified table.
`list_quantum_systems`	read	List all available quantum systems.
`moire_homobilayer`	read
`nemad_formula_search`	read	Search for materials by exact chemical formula in NEMAD database.
`nemad_list_cache`	read	List all available cached search results.
`nemad_read_results`	read	Read specific range of cached search results.
`nemad_search`	read	Search for materials by elements in NEMAD database.
`parameter_sweep`	read	Perform a parameter sweep for a quantum model.
`plot_structure`	read
`plot_xy`	write	Generate a generic 2D plot and save it to a file.
`purge_table`	destructive	Removes all documents from the specified table.
`query_documents`	read	Queries documents from the specified table.
`read-image-url`	read	Read images from URLs, convert to base64, and return the image content.
`search_materials_by_formula`	read
`select_material_by_id`	read
`set_hamiltonian`	write	Set the Hamiltonian for a quantum system with optional parameter ranges for sweeps.
`set_hilbert_space`	write	Set the Hilbert space for a quantum system.
`set_lattice`	write	Set the lattice geometry for a quantum system.
`start_calculation`	write
`txyz_search_smart`	read	return await _search(
`txyz_search_web`	read	return await _search(
`update_documents`	write	Updates documents in the specified table.
`verify_derivation`	read

Trust audit

CAUTIONgrade B · trust 86/100 Install with care. The audit found things worth knowing before you trust its output.

Layer	What it checks	Result
L0	Provenance & inventory	PASS
L1	Static analysis of the code	WARN
L2	Instruction surface (what it tells the agent)	PASS
L3	Class-specific surface	WARN
L4	Behavioural (sandbox)	SKIPPED

What the source does

Filesystem: declared (5 observation(s))
Network: declared (5 observation(s))
Shell: declared (1 observation(s))
Dependencies: pinned
Secrets in source: none-found

Findings (18)

MEDIUMCode injection · code.dynamic_import · CWE-78, CWE-94, CWE-95

servers/python-code-execution/src/python_code_execution/local_python_executor.py:1106

raw_module = __import__(expression.module, fromlist=[

MEDIUMObfuscation / stealth · obf.base64_blob · CWE-506, CWE-94

servers/example-server/src/example_server/main.py:37

image_base64 = "iVBORw0KGgoAAAANSUhEUgAAAB4AAAAeCAYAAAA7MK6iAAAAIGNIUk0AAHomAACAhAAA+gAAAIDoAAB1MAAA6mAAADqYAAAXcJy6UTwAAAAGYktHRAD/AP8A/6C9p5MAAAAJcEhZcwABGUAAARlAAYDjddQAAAAHdElNRQfpBBUNAgfLUoX1AAAA

MEDIUMFilesystem / path · mcp.destructive_tools · CWE-22, CWE-59

delete_documents, delete_quantum_system, drop_table, purge_table

Why it matters. 4 tool(s) can delete or overwrite

Fix. prefer a read-only mode or scoped tokens; the page states the blast radius