Scispot MCP

Scispot MCP Server

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

Use with Cursor

This repository is also a Cursor plugin. It connects Cursor's agent to Scispot's hosted MCP server at https://mcp.scispot.io/ (streamable HTTP).

Install

1. Open Cursor Settings → Plugins.
2. Search for Scispot and click Install.
3. When Cursor connects to the server, it opens the Scispot sign-in page in your browser. Sign in with your Scispot account to authorize the connection (OAuth). There is no API key to paste into Cursor.

Or run /add-plugin scispot in chat.

The plugin adds this MCP server:

{

"mcpServers": { "scispot": { "type": "http", "url": "https://mcp.scispot.io/" } } }

Requirements

• A Scispot account with Super Admin access, or an account with Dry Lab access.
• Tool calls run with your Scispot permissions. The agent can see and change only what your account allows.

Example prompts

• "List my Scispot Labsheets."
• "Show the schema of the 'Cell Lines' Labsheet, then find rows where Status is 'Active'."
• "List the protocols in the 'Genomics' Labspace and summarize the 'DNA Extraction SOP' protocol."
• "Look up the manifest with barcode 'PLT-00142' and show which wells are filled."
• "Create an experiment called 'Western Blot Optimization Round 3' in the 'Protein Lab' Labspace and add a summary of today's run."

Start with a read-only request such as "List my Scispot Labsheets" to confirm the connection.

Write tools

Start with read-only requests. Review the data and the planned action before you approve a write.

For important records, ask the agent to summarize the proposed changes before it creates or updates data. Review the resulting record in Scispot after the action completes.

Eight tools are marked destructive because they overwrite existing rows or page content: update_labsheet_rows, update_labsheet_rows_by_id_column, write_to_experiment, write_to_protocol, write_to_documentation, and link_manifest_to_* (when position is replace).

For regulated workflows, make sure your use of Cursor and its data handling meets your organization's validation, review, and approval requirements.

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 55 tools spanning Labsheet data management, Electronic Lab Notebook (ELN) operations, inventory/storage lookups, Labflow sample tracking, and Jazz apps. 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 Labspaces and folders, and create folders for ELN pages.
• Tags — List tag categories, search tag values, and set tags on ELN pages.
• Jazz apps — Read the build guide, then list, create, upload, publish, and roll back custom Jazz apps.

Setup

Choose MCP or the REST API

Use the MCP Server when you want an AI assistant to work with Scispot conversationally. Use the REST API when you build a programmatic integration or automation.

Before you begin

You need:

• A Super Admin Scispot account, or an account with Dry Lab access
• An MCP-compatible AI client

The MCP Server uses https://mcp.scispot.io.

Security and permissions

The MCP Server respects your existing Scispot permissions. You can access only the data and actions that your Scispot account allows.

Web connectors use OAuth. Sign in with your Scispot account when the client asks you to authorize the connection.

Connect Claude.ai

Use Claude.ai's custom connector flow. Sign in with your Scispot account when prompted.

1. In Claude.ai, open Settings, then Connectors. Select Add custom connector.
2. Search for Scispot.io in the connector search bar.
3. Click Connect to Claude.
4. Complete authentication by logging in with your Scispot account.

Test the connection with a read-only request such as: "List my Scispot Labsheets."

Connect Claude Code

Claude Code supports remote MCP servers over HTTP. Add Scispot as an HTTP MCP server, then authenticate in the client.

1. In your terminal, run:

claude mcp add --transport http scispot-mcp https://mcp.scispot.io/

1. Open Claude Code with the claude command.
2. Enter /mcp to check your MCP connections.
3. Select the scispot-mcp connection, choose Authenticate, and log in with your Scispot account.
4. Start or restart Claude Code. Ask it to list your Scispot Labsheets to confirm that it can discover the server tools.

Test the connection with a read-only request such as: "List my Scispot Labsheets."

Connect another MCP-compatible client

You can connect other clients that support remote HTTP MCP servers. The exact labels vary by client.

1. Add a remote MCP server or connector in your client.
2. Set the connection URL to https://mcp.scispot.io.
3. Choose OAuth when your client supports the Scispot OAuth flow.
4. When prompted, log in with your Scispot account.
5. Confirm the connection with a read-only request before you perform a write operation.

Contact Customer Success at cs@scispot.io if your client cannot complete the OAuth flow or does not support custom HTTP headers.

Use write actions safely

Start with read-only requests. Review the data and the planned action before you approve a write.

For important records, ask the AI to summarize the proposed changes before it creates or updates data. Review the resulting record in Scispot after the action completes.

Tools that change data require the same permissions as the equivalent action in Scispot. Eight tools are marked destructive because they overwrite existing rows or page content: update_labsheet_rows, update_labsheet_rows_by_id_column, write_to_experiment, write_to_protocol, write_to_documentation, and link_manifest_to_* (when position is replace).

For regulated workflows, make sure your use of the AI client and its data handling meets your organization's validation, review, and approval requirements.

Troubleshooting

You cannot add the connector

Verify that you entered https://mcp.scispot.io exactly.

Authentication fails

Contact Customer Success at cs@scispot.io if you cannot authenticate.

You cannot see data or perform an action

The MCP Server uses your Scispot permissions. Confirm that you can complete the same action in Scispot with your account.

The AI proposes an unexpected change

Do not approve the action. Ask the AI to explain the proposed change, then verify the target records in Scispot before you continue.

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

Tools below match the production server at https://mcp.scispot.io/ (55 tools). Destructive follows the server's destructiveHint: those calls can overwrite existing rows or page content.

Read-Only Tools (27)

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