How to Use the GenBank/NCBI API MCP in Windsurf

Connect Windsurf to the world's largest genomic database. Let Cascade automate sequence discovery using this MCP Server.

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Connect GenBank/NCBI API MCP to Windsurf

Create your Vinkius account to connect GenBank/NCBI API to Windsurf and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup GenBank/NCBI API with Windsurf

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Find Any Sequence, Instantly

This tool connects your agent directly to NCBI's core search. Give Cascade a goal like "Find human BRCA1 protein sequences" and it uses `search_ncbi_sequences` to get all the relevant UIDs from the 'protein' database. No more manual web searches. Windsurf won't just give you a list of IDs and stop. It sees the UIDs as the next step and automatically feeds them into other tools, like `get_ncbi_summary`, to pull metadata for each one. That's the point of an autonomous agent connected to a powerful MCP.

Get Sequence Summaries with Windsurf

Once you have a list of sequence UIDs, you need to know what they are. The `get_ncbi_summary` tool fetches the summary for any given ID. This includes definitions, molecular type, length, and modification dates. This is where Cascade shines. It can take a hundred UIDs from a search, loop through them, and call `get_ncbi_summary` for each one. You get a full report without writing a single line of code or a single follow-up prompt.

Explore NCBI Databases with this MCP Server

NCBI has more than just nucleotide and protein databases. Use `list_ncbi_databases` to see everything available, from gene and genome information to SNP and structure data. It's a quick way to discover what you can actually search. Before you run a complex workflow, have your agent ping the `check_api_status` tool. This confirms the NCBI E-utilities are up and running. It's a simple step that prevents a lot of failed runs.

Setup guide

Set up GenBank/NCBI API MCP in Windsurf

Prerequisites

Windsurf IDE installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Click the Cascade assistant icon in the sidebar, then click the hammer icon (🔨) at the top of the panel. Select "Configure" to open ~/.codeium/windsurf/mcp_config.json.
2

Add the GenBank/NCBI API MCP

Paste the JSON snippet shown on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Refresh MCPs

Go back to the hammer icon (🔨) in Cascade and click "Refresh". Windsurf will detect the new server. No full restart is needed — the connection is hot-reloaded.
4

Verify in Cascade

Start a new Cascade conversation and ask something like "Show my GenBank/NCBI API payment history." If connected, Cascade will call the GenBank/NCBI API tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

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

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by GenBank/NCBI. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about GenBank/NCBI API MCP in Windsurf

Just ask Cascade. For example: "Using the GenBank/NCBI API, find all nucleotide sequences for the human MTHFR gene." Windsurf will use `search_ncbi_sequences` through this MCP Server to get the job done.

Yes. Give Windsurf the list of UIDs and ask it to "get summaries for these IDs." It will automatically chain calls to the `get_ncbi_summary` tool for each ID in your list.

No problem. Tell Windsurf to "list all available NCBI databases." It will run the `list_ncbi_databases` tool and show you all your options so you can pick the right one for your next search.

Simply prompt Windsurf: "Check the NCBI API status." It will use the `check_api_status` tool and tell you if the service is operational before you waste time on a long-running query.

Your search terms and the resulting sequence UIDs are passed through the MCP server, but it's an ephemeral, sandboxed environment. Vinkius manages the secure connection and doesn't store your query data.

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