Scispot MCP Server

Connect Claude to your Scispot lab workspace — query Labsheets, manage ELN experiments, protocols, documentation, storage locations, manifests, and more, all through natural language.

Description

The Scispot MCP Server is a remote Model Context Protocol (MCP) server that integrates Scispot's Lab Operating System with AI assistants like Claude. It provides 27 tools spanning Labsheet data management, Electronic Lab Notebook (ELN) operations, inventory/storage lookups, and Labflow sample tracking. The server runs as an AWS Lambda function and authenticates via OAuth 2.0 with PKCE.

Features

Labsheet Management — List, search, and filter Labsheet rows; inspect schemas; add and update data; organize by folders.
ELN Experiments — List, read, create, and write content to experiments; link Labsheet rows for traceability.
ELN Protocols — List, read, create, and write structured content (text, sections, files, images) to protocols; link Labsheet rows.
ELN Documentation — List, read, create, and write to documentation entries; link Labsheet rows.
Storage & Inventory — Browse storage locations (freezers, rooms, cabinets) and fetch manifests (plates, boxes, racks) by ID or barcode.
Labflows — List sample UUIDs associated with a Labflow for downstream analysis.
Labspaces — Discover all available Labspaces as the entry point for ELN navigation.

Setup

Claude web app (Anthropic MCP Directory)

Use these steps when using Claude in the browser (claude.ai), not Claude Code.

Visit the Anthropic MCP Directory
Find and connect to Scispot
Complete OAuth authentication using your Scispot API key
Start interacting with your workspace through Claude

Claude Code (terminal)

From a terminal, register the remote MCP server with Claude Code using your Scispot API key:

Terminal

claude mcp add scispot https://mcp.scispot.io/ --transport http --header "Authorization: Bearer YOUR_SCISPOT_API_KEY"

Replace YOUR_SCISPOT_API_KEY with your actual API key. Restart Claude Code or reload MCP configuration if prompted so the new server is picked up.

Authentication

This server requires OAuth 2.0 authentication with PKCE (S256). During the connection flow:

You will be prompted to provide your Scispot API key as the client secret
The API key is used solely as a Bearer token for Scispot API requests
No credentials are persisted to permanent storage on the server
Authorization codes expire within 5 minutes

You need a valid Scispot account with API access. Contact your Scispot administrator if you need an API key.

Examples

Example 1: Explore and query Labsheet data

User prompt: "Show me all the Labsheets in my workspace, then find the schema for the 'Cell Lines' Labsheet and search for rows where the Status column equals 'Active'."

What happens:

Server calls list_labsheets to return all available Labsheets
Server calls get_labsheet_schema for "Cell Lines" to discover column names and types
Server calls search_labsheet_rows with a mandatory filter on the Status column
Returns matching rows with all column data

Example 2: Create an experiment and write a protocol summary

User prompt: "Create a new experiment called 'Western Blot Optimization Round 3' in the 'Protein Lab' Labspace, then write a summary of the protocol steps I'll be using."

What happens:

Server calls list_labspaces to confirm "Protein Lab" exists and get its location
Server calls create_experiment_stub with the name and location
Server calls write_to_experiment to append the protocol summary as HTML content
Returns confirmation with the new experiment details

Example 3: Link Labsheet samples to a protocol with structured content

User prompt: "Find all samples in the 'Reagent Inventory' Labsheet where the Lot Number is 'LOT-2025-001', link them to the 'Sample Preparation v2' protocol in the 'QC Lab' Labspace, and add a structured section to the protocol documenting the linked samples."

What happens:

Server calls search_labsheet_rows to find matching rows in "Reagent Inventory"
Server calls link_labsheet_to_protocol to create traceability links between the rows and the protocol
Server calls write_to_protocol with content_type='json' and a structured elements array containing a section header and text descriptions
Returns confirmation of linked rows and updated protocol content

Example 4: Browse storage locations and fetch a manifest

User prompt: "Show me all storage locations in my workspace, then look up the manifest with barcode 'PLT-00142'."

What happens:

Server calls list_locations to return all root-level storage locations (freezers, rooms, cabinets)
Server calls get_manifest with the barcode to fetch the plate/container details including all wells or slots
Returns the full manifest layout with sample positions

Example 5: Navigate ELN structure and read documentation

User prompt: "List all Labspaces, then show me the protocols in the 'Genomics' Labspace, and read the full content of the 'DNA Extraction SOP' protocol."

What happens:

Server calls list_labspaces to discover available Labspaces
Server calls list_protocols with location "Genomics" to list all protocols
Server calls get_protocol by name to fetch the full protocol content
Returns the complete protocol text with formatting

Available Tools

Read-Only Tools (16)

Tool	Description
`list_labsheets`	List all Labsheets in the workspace
`get_labsheet_schema`	Get column definitions for a Labsheet
`search_labsheet_rows`	Search and filter Labsheet rows
`get_labsheet_row`	Fetch a single row by UUID
`list_labsheet_folders`	List folders or Labsheets within a folder
`list_labspaces`	List all ELN Labspaces
`list_experiments`	List experiments in a location
`get_experiment`	Fetch full experiment content
`list_protocols`	List protocols in a location
`get_protocol`	Fetch full protocol content
`list_documentations`	List documentation entries in a location
`get_documentation`	Fetch full documentation content
`list_locations`	List root-level storage locations
`get_manifest`	Fetch a manifest by hrid, uuid, or barcode
`list_labflow_samples`	List sample UUIDs for a Labflow
`get_image_thumbnail`	Download a row's image thumbnail

Write Tools (11)

Tool	Destructive	Description
`add_labsheet_rows`	No	Add new rows to a Labsheet
`update_labsheet_rows`	Yes	Overwrite existing row values
`create_experiment_stub`	No	Create an empty experiment
`write_to_experiment`	Yes	Append/prepend content to an experiment
`create_protocol_stub`	No	Create an empty protocol
`write_to_protocol`	Yes	Write text, structured JSON, or images to a protocol
`create_documentation_stub`	No	Create an empty documentation entry
`write_to_documentation`	Yes	Append/prepend content to documentation
`link_labsheet_to_experiment`	No	Link Labsheet rows to an experiment
`link_labsheet_to_protocol`	No	Link Labsheet rows to a protocol
`link_labsheet_to_documentation`	No	Link Labsheet rows to documentation

Privacy Policy

This MCP server processes only the data necessary to execute requested operations against your Scispot workspace. No conversation data is collected or stored.

For complete privacy information, see our privacy policy: https://www.scispot.com/legal/privacy-policy

Support

Email: team@scispot.io
API Documentation: https://docs.scispot.com/
Website: https://www.scispot.com