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:
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_labsheetsto return all available Labsheets - Server calls
get_labsheet_schemafor "Cell Lines" to discover column names and types - Server calls
search_labsheet_rowswith 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_labspacesto confirm "Protein Lab" exists and get its location - Server calls
create_experiment_stubwith the name and location - Server calls
write_to_experimentto 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_rowsto find matching rows in "Reagent Inventory" - Server calls
link_labsheet_to_protocolto create traceability links between the rows and the protocol - Server calls
write_to_protocolwithcontent_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_locationsto return all root-level storage locations (freezers, rooms, cabinets) - Server calls
get_manifestwith 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_labspacesto discover available Labspaces - Server calls
list_protocolswith location "Genomics" to list all protocols - Server calls
get_protocolby 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