Elnora MCP Server

Elnora MCP Server

Connect AI agents to the Elnora bioprotocol optimization platform via the Model Context Protocol.


What is Elnora?

Elnora is an AI-powered platform that helps researchers generate, optimize, and manage bioprotocols for wet-lab experiments. With this MCP server, you can interact with Elnora directly from AI coding assistants like Claude Code, Cursor, VS Code, Codex, and ChatGPT.

Quick Start

Add the Elnora MCP server to your AI client. No installation required — just point to the remote URL.

Setting this up from inside a coding agent? See INSTALL_FOR_AGENTS.md for a step-by-step, self-verifying runbook (client config, auth, and a smoke test).

Claude Code

claude mcp add elnora --transport http --scope user https://mcp.elnora.ai/mcp

Installation scopes:

| Scope | Flag | Where it's stored | Best for | |-------|------|--------------------|----------| | User | --scope user | ~/.claude.json | Available in all your projects (recommended) | | Local | --scope local | Current project config | Single-project use (default if omitted) | | Project | --scope project | .mcp.json in project root | Team sharing via version control |

Cursor

Add to your Cursor MCP settings (Settings > MCP Servers):

{
  "mcpServers": {
    "elnora": {
      "url": "https://mcp.elnora.ai/mcp"
    }
  }
}

VS Code (Copilot)

Add to your .vscode/mcp.json:

{
  "servers": {
    "elnora": {
      "type": "http",
      "url": "https://mcp.elnora.ai/mcp"
    }
  }
}

Codex

codex --mcp-config mcp.json

With mcp.json:

{
  "mcpServers": {
    "elnora": {
      "url": "https://mcp.elnora.ai/mcp"
    }
  }
}

ChatGPT

Add as a remote MCP server in ChatGPT settings using the URL https://mcp.elnora.ai/mcp.

---

On first connection, a browser window will open for OAuth login. Subsequent requests use the issued token automatically.

Authentication

OAuth 2.1 (Recommended)

Most MCP clients handle OAuth automatically. On first connection:

1. A browser window opens for login
2. You authenticate with your Elnora account
3. The client receives a token and uses it for subsequent requests

No manual configuration needed.

API Key

Create an API key in your Elnora dashboard and pass it via the X-API-Key header:

{
  "mcpServers": {
    "elnora": {
      "url": "https://mcp.elnora.ai/mcp",
      "headers": {
        "X-API-Key": "YOUR_API_KEY"
      }
    }
  }
}

If your client only exposes a single bearer/token field, you can instead pass the same key as Authorization: Bearer YOUR_API_KEY — the server accepts an Elnora API key on either header.

Security best practices:

• Never commit API keys to version control
• Use environment variables or a secrets manager
• Rotate keys periodically via the Elnora dashboard
• Use OAuth when possible — it handles token refresh automatically

Capabilities

74 tools across 15 categories. All tools are discoverable through your MCP client's tool listing.

| Category | Tools | What you can do | |----------|------:|-----------------| | Protocols | 1 | Generate optimized bioprotocols from natural language descriptions | | Tasks | 6 | Create conversation threads, send messages, get AI responses | | Messages | 1 | Chat with Elnora's AI within a task context | | Files | 18 | Upload, download, version, fork, and manage protocol files | | Projects | 10 | Create projects and manage team membership | | Organizations | 13 | Org settings, billing, member invitations | | Folders | 5 | Organize files into nested folder structures | | Library | 5 | Access the organization's shared protocol library | | Search | 3 | Full-text search across tasks, files, and all resources | | API Keys | 3 | Create and manage personal API keys | | Audit | 1 | Query organization audit logs | | Account | 4 | Manage user profile and agreements | | Feedback | 1 | Submit platform feedback | | Feature Flags | 2 | Check feature availability | | Health | 1 | Verify API connectivity |

Examples

Generate a bioprotocol

"Use Elnora to generate a HEK 293 cell maintenance protocol"

The assistant will call elnora_generate_protocol with your description and return the generated protocol. This can take 30-120s for complex requests.

Search and read files

"List my files in Elnora, then show me the content of the most recent protocol"

Manage tasks

"Show me my active Elnora tasks and get the messages from the latest one"

Organize a project

"Create a new project called 'Q3 Assays', add a folder for each cell line, and invite alex@example.com"

Troubleshooting

| Error | Cause | Solution | |-------|-------|----------| | 401 Unauthorized | Missing or expired token | Re-authenticate via OAuth or check your API key | | 403 Forbidden | Insufficient permissions | Verify your account has access to the requested resource | | 408 / Timeout | Complex operation taking too long | Protocol generation can take up to 120s — try again or simplify the request | | Connection refused | Server unreachable | Check your internet connection; verify https://mcp.elnora.ai/health is accessible |

If you encounter persistent issues, please open a GitHub issue.

Security

We take security seriously. If you discover a vulnerability, please report it responsibly — see our security policy.

Contributing

See CONTRIBUTING.md for contribution guidelines.

Changelog

See CHANGELOG.md for version history.

License

Apache License 2.0

Support

• Bug reports and feature requests: GitHub Issues
• Account and billing: support@elnora.ai
• Security vulnerabilities: security@elnora.ai