Is an API Key required for GenBank/NCBI API?

No. The NCBI E-utilities API is a free and open service provided by the United States government. This server works out of the box without any static credentials required.

Which databases are supported?

The API supports multiple databases including 'nuccore' (Nucleotide), 'protein', 'pubmed', and 'gene'. Use the `list_ncbi_databases` tool to see the full list.

A UID is a unique identifier assigned to each record in an NCBI database. Your agent uses these UIDs to retrieve specific summaries and detailed metadata.

GenBank/NCBI API MCP Server for Windsurf 4 tools — connect in under 2 minutes

Name: GenBank/NCBI API
Availability: InStock
Author: Vinkius

docs.windsurf.com/windsurf/mcp

Built by Vinkius GDPR 4 Tools IDE

Windsurf brings agentic AI coding to a purpose-built IDE. Connect GenBank/NCBI API through Vinkius and Cascade will auto-discover every tool. ask questions, generate code, and act on live data without leaving your editor.

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Classic Setup·json

{
  "mcpServers": {
    "genbankncbi-api": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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About GenBank/NCBI API MCP Server

Empower your AI agent to orchestrate your entire biological research and genomic auditing workflow with the GenBank/NCBI API, the authoritative source for molecular biology data from the National Center for Biotechnology Information. By connecting NCBI's E-utilities to your agent, you transform complex sequence searches into a natural conversation. Your agent can instantly retrieve sequence UIDs, audit bibliographic summaries, and query protein metadata without you ever touching a bioinformatics portal. Whether you are conducting evolutionary research or managing laboratory constraints, your agent acts as a real-time genomic consultant, ensuring your data is always verified and precise.

Windsurf's Cascade agent chains multiple GenBank/NCBI API tool calls autonomously. query data, analyze results, and generate code in a single agentic session. Paste Vinkius Edge URL, reload, and all 4 tools are immediately available. Real-time tool feedback appears inline, so you see API responses directly in your editor.

What you can do

Sequence Auditing — Search for thousands of genetic sequences by keyword and retrieve high-resolution metadata, including UIDs and titles.
Database Oversight — Audit multiple NCBI databases like 'nuccore' or 'protein' to understand the thematic distribution of biological data instantly.
Summary Discovery — Query technical and bibliographic summaries for specific sequence IDs to assist in deep-dive archival classification.
Metadata Intelligence — Retrieve unique identifiers and caption details for any biological record to assist in scientific auditing.
Operational Monitoring — Check API status to ensure your bioinformatics research workflow is always operational.

The GenBank/NCBI API MCP Server exposes 4 tools through the Vinkius. Connect it to Windsurf in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect GenBank/NCBI API to Windsurf via MCP

Follow these steps to integrate the GenBank/NCBI API MCP Server with Windsurf.

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"

Add the server

Paste the JSON configuration above into mcp_config.json

Save and reload

Windsurf will detect the new server automatically

Start using GenBank/NCBI API

Open Cascade and ask: "Using GenBank/NCBI API, help me...". 4 tools available

Why Use Windsurf with the GenBank/NCBI API MCP Server

Windsurf provides unique advantages when paired with GenBank/NCBI API through the Model Context Protocol.

Windsurf's Cascade agent autonomously chains multiple tool calls in sequence, solving complex multi-step tasks without manual intervention

Purpose-built for agentic workflows. Cascade understands context across your entire codebase and integrates MCP tools natively

JSON-based configuration means zero code changes: paste a URL, reload, and all 4 tools are immediately available

Real-time tool feedback is displayed inline, so you see API responses directly in your editor without switching contexts

GenBank/NCBI API + Windsurf Use Cases

Practical scenarios where Windsurf combined with the GenBank/NCBI API MCP Server delivers measurable value.

Automated code generation: ask Cascade to fetch data from GenBank/NCBI API and generate models, types, or handlers based on real API responses

Live debugging: query GenBank/NCBI API tools mid-session to inspect production data while debugging without leaving the editor

Documentation generation: pull schema information from GenBank/NCBI API and have Cascade generate comprehensive API docs automatically

Rapid prototyping: combine GenBank/NCBI API data with Cascade's code generation to scaffold entire features in minutes

GenBank/NCBI API MCP Tools for Windsurf (4)

These 4 tools become available when you connect GenBank/NCBI API to Windsurf via MCP:

check_api_status

Check if the NCBI E-utilities service is operational

get_ncbi_summary

Get a summary for a specific NCBI sequence ID

list_ncbi_databases

List all available NCBI databases

search_ncbi_sequences

g., nuccore, protein) based on a query term. Search for biological sequences in an NCBI database

Example Prompts for GenBank/NCBI API in Windsurf

Ready-to-use prompts you can give your Windsurf agent to start working with GenBank/NCBI API immediately.

"Search for 'human insulin' in the 'protein' database using NCBI."

"Get the summary for NCBI UID '123456' in 'nuccore'."

"List all available NCBI databases."

Troubleshooting GenBank/NCBI API MCP Server with Windsurf

Common issues when connecting GenBank/NCBI API to Windsurf through the Vinkius, and how to resolve them.

Server not connecting

Check Settings → MCP for the server status. Try toggling it off and on.

GenBank/NCBI API + Windsurf FAQ

Common questions about integrating GenBank/NCBI API MCP Server with Windsurf.

How does Windsurf discover MCP tools?

Windsurf reads the mcp_config.json file on startup and connects to each configured server via Streamable HTTP. Tools are listed in the MCP panel and available to Cascade automatically.

Can Cascade chain multiple MCP tool calls?

Yes. Cascade is an agentic system. it can plan and execute multi-step workflows, calling several tools in sequence to accomplish complex tasks without manual prompting between steps.

Does Windsurf support multiple MCP servers?

Yes. Add as many servers as needed in mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.