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Scispot MCP Server

Control Your Lab with AI — From Any LLM

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Written by Satya Singh

What Is This?

The Scispot MCP (Model Context Protocol) Server allows you to connect Scispot with your preferred AI assistant, including Claude, ChatGPT, Gemini, and other MCP-compatible platforms. Once connected, you can interact with your Scispot lab workspace using natural language to ask questions, update data, create experiments, analyze results, and perform other workspace operations — all through simple conversational prompts, with no coding required.
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Connection Requirements: Only Super Admin accounts can directly authorize and establish an MCP connection. Non-Super Admin users will need a Super Admin to complete the initial connection through their preferred AI assistant. Access and available functionality are then governed by the workspace and token permissions configured during authorization.

Key Features:

✅ Works with Claude, ChatGPT, Gemini, and other MCP compatible platforms

✅ Secure OAuth authentication

✅ 50+ powerful tools for labsheets, experiments, samples, and protocols

✅ Read and write access (with your existing permissions)
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Quick Start

Prerequisites

  • An active Scispot Super Admin account

  • Claud, ChatGPT, Gemini, or Cursor installed

Setup Instructions Example

Setup Scispot MCP connector on the web (Claude.ai)

  1. Navigate to Connectors: In Claude.ai, open the Customize tab from the left-hand sidebar.​

  2. Open the Connectors page: Select Connectors from the top navigation bar.
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  3. Find Scispot.io: Use the search bar to search for Scispot.io.

  4. Initiate the connection: Select the Scispot.io connector and click Connect to Claude. You will be redirected to the Scispot login page.

  5. Log in to Scispot: Sign in using your Scispot account credentials.

    • Super Admin access is required to establish the MCP connection.

    • If you are not a Super Admin, you will need a Super Admin to log in and enable the MCP connection on your behalf.

  6. Configure workspace and token permissions: Once logged in, select the appropriate Workspace and configure the token access permissions.

    • Follow the organization's token access guidelines.

    • Grant only the permissions necessary for the intended use of the MCP.

    • Ensure that token permissions align with the user's required access level to prevent unintended access to restricted data or functionality.

  7. Complete the connection: Review your workspace and permission selections, then complete the authorization process by clicking Allow to finish connecting Scispot.io to Claude.

Setup Scispot MCP connector on Claude Code (Terminal)

  1. Add the Scispot MCP server: Run the following command to add the Scispot MCP connector to Claude Code
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    claude mcp add scispot-mcp https://mcp.scispot.io/ --transport http

  2. Open Claude Code: Start Claude Code and run the /mcp command to view the list of configured MCP servers.

  3. Verify the connection status: Locate scispot-mcp in the list of MCP servers. Its status should indicate Needs Authorization, meaning the server is ready for authentication.

  4. Initiate authentication: Select the scispot-mcp server and choose the Authenticate option to begin the authorization process.
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  5. Log in to Scispot: You will be redirected to the Scispot login page.

    • Super Admin access is required to complete the MCP connection.

    • Users without Super Admin privileges will need a Super Admin to complete the authorization process on their behalf.
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  6. Select workspace and configure permissions: After logging in, the Super Admin must select the appropriate Workspace and configure the token access permissions.

    • Follow the organization's token access guidelines.

    • Grant only the permissions required for the intended MCP functionality.

  7. Complete the authorization: Once the workspace and token permissions have been selected and authorized, return to Claude Code. The Scispot MCP connection should now be ready to use.
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What You Can Do

Ask Questions in Plain English

  • "Show me all samples in the -80°C freezer"

  • "What experiments did Sarah run last week?"

  • "Which assays have TAT over 48 hours?"

  • "Find all samples where Status=Active AND Concentration > 10mg/mL"

  • "Look at experiment EXP-042, research related publications, and suggest protocol updates"

Automate Routine Tasks

  • Update hundreds of labsheet rows with a single prompt

  • Generate experiment documentation from voice notes

  • Cross-reference protocols, materials, and results

  • Track sample locations across your facility

  • Bulk-add QC results from instrument outputs

Get Instant Insights

  • Search across all labsheets, experiments, and protocols simultaneously

  • Filter and analyze data without writing queries

  • Link experimental data to inventory and documentation

  • Access your entire lab knowledge base conversationally

For Every Lab Role

🧪 Wet Lab Scientists

Spend less time on data entry, more time at the bench.

  • Voice-to-data: "Add 12 new mouse samples to the breeding colony tracker with these IDs..."

  • Quick lookups: "Where is the anti-FLAG antibody stored?" → Get location, lot number, and expiration instantly

  • Protocol access: "Show me the latest cell culture protocol for HEK293 cells"

  • Documentation: "Create an experiment note for today's Western blot with these observations..."

No coding required. Just ask in natural language.

💻 Computational Scientists & Bioinformaticians

Accelerate data analysis workflows.

  • Batch operations: Update metadata for thousands of sequencing runs

  • Data integration: Cross-reference NGS results with sample metadata from labsheets

  • Automated reporting: Generate sample manifests, QC reports, and data summaries

  • Schema exploration: Discover available data fields and relationships without SQL

API-like power with conversational simplicity.

📊 Lab Managers & Operations

Stay on top of inventory, compliance, and throughput.

  • Inventory monitoring: "Which reagents expire in the next 30 days?"

  • Capacity planning: "How many samples are pending QC review?"

  • Team productivity: "List all experiments created"

Real-time visibility without dashboards or reports.

🔬 Principal Investigators

Oversee research progress conversationally.

  • Project overview: "Summarize all experiments for the kinase inhibitor project"

  • Resource allocation: "Which equipment has been most utilized this quarter?"

  • Data exploration: "Find all assays with IC50 values below 10nM"

  • Collaboration: "Show me protocols shared between the Boston and Cambridge sites"

Strategic insights without digging through folders.

AI Platform Support

Compatible AI Assistants

The Scispot MCP Server works with all major AI platforms that support the Model Context Protocol:

Platform

Setup Method

Best For

Claude Desktop

OAuth (one-click)

Complex reasoning, multi-step workflows

ChatGPT Plus

Third-party integration

Broad familiarity, mobile access

Gemini Advanced

Extension marketplace

Fast responses, multimodal queries

Cursor / VS Code

MCP extension

Developers, computational biologists

You choose the AI model that fits your budget and performance needs. Switch between models seamlessly without changing your Scispot integration.

Security & Compliance

Enterprise-Grade Security

Your data security is our top priority. The Scispot MCP Server is built with multiple layers of protection:

Authentication & Authorization

  • OAuth 2.0 + PKCE: Industry-standard authentication protocol used by Google, Microsoft, and major financial institutions

  • Personal access tokens: Each user generates their own access token — no shared credentials

  • Token expiration: Automatic token lifecycle management

  • Scope-based permissions: Tools only access data you explicitly authorize

Data Protection

  • Encrypted transit: All data transmitted over HTTPS/TLS 1.3

  • No training data: Your proprietary lab data is never used to train AI models

  • AWS infrastructure: Hosted on AWS with SOC 2, HIPAA-eligible, and ISO 27001 compliance

  • Audit logging: All API calls are logged with user identity, timestamp, and action details

What the AI Can and Cannot Do

✅ The AI assistant can:

  • Read data you have permission to view

  • Create and modify labsheet rows

  • Create and append to experiments

  • Search across your accessible data

❌ The AI assistant cannot:

  • Access data outside your Scispot account

  • Delete labsheets or experiments (read/create/update only)

  • Change user permissions or system settings

  • Export data outside Scispot without your explicit command

  • Execute arbitrary code or system commands

You remain in control. You can review every action before it executes, and all changes are traceable in Scispot's audit log.

HIPAA & Regulatory Compliance

Important: Scispot infrastructure supports HIPAA workloads and FDA 21 CFR Part 11 requirements. Contact [email protected] for a Business Associate Agreement (BAA) if you handle PHI.

Customer responsibility: When using external AI models (Claude, ChatGPT, Gemini), you are responsible for ensuring compliance with your data handling policies. The MCP connection provides secure access, but data sent to external AI providers is governed by their terms of service.

For regulated environments, we recommend:

  • Using Claude for Enterprise or ChatGPT Enterprise with BAAs

  • Reviewing your organization's AI usage policies

  • Training staff on what data can be shared with AI assistants

FAQ

General

Q: Do I need to know how to code?
A: No. Just ask in natural language — the AI handles everything.

Q: Which AI platform is best?
A: It depends on your needs. Claude excels at complex reasoning, ChatGPT has broad adoption, and Gemini offers competitive pricing. Many teams use multiple models.

Q: Can I use this on mobile?
A: Yes, if your AI platform has a mobile app (Claude and ChatGPT both do).

Q: Does this work offline?
A: No. The integration requires internet access to query your Scispot workspace.

Security

Q: Can I audit what the AI does?
A: Yes. All API calls are logged in Scispot with user, timestamp, and action details. Go to Settings → Audit Log to review.

Q: Is this HIPAA compliant?
A: Scispot infrastructure supports HIPAA workloads. Contact us for a Business Associate Agreement (BAA) if you handle PHI. Important: You are responsible for compliance when data is sent to external AI models (Claude, ChatGPT, etc.). Use enterprise AI plans with BAAs for regulated data.

Q: What if someone unauthorized gets my OAuth token?
A: Tokens expire automatically and are scoped to your permissions. You can revoke access anytime in Settings → Connected Apps. All actions are logged.

Technical

Q: What if the AI makes a mistake?
A: You can undo changes via Scispot's revision history. For critical operations, we recommend reviewing AI-generated changes before confirming.

Q: Can I integrate this with my own scripts?
A: Yes. The MCP server can be called from any MCP-compatible client, including custom applications. See the technical documentation for details.

Q: What's the difference between this and the Scispot API?
A: The MCP server is designed for conversational AI access. The REST API is for programmatic integrations. Both use the same underlying data and permissions.

Q: Can I use this in a regulated GxP environment?
A: Yes, with caveats. Scispot supports 21 CFR Part 11, but AI-generated content must be reviewed by qualified personnel before signing off. Contact [email protected] for validation support packages.

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