How to Use the KEGG MCP in Windsurf

Q: How do I search for KEGG pathways in Windsurf?

Use the keggfind tool via the Cascade sidebar. Just ask your agent to search for a specific keyword or chemical identifier and it will return the matching entries.

Q: Can I use KEGG to list all organisms in Windsurf?

Absolutely. Just instruct Cascade to run kegglist with the 'organism' parameter. It will fetch the full list of supported KEGG organisms for your analysis.

Cascade chains KEGG genomic queries directly in your Windsurf editor for faster pathway analysis.

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Connect KEGG MCP to Windsurf

Create your Vinkius account to connect KEGG 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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Autonomous pathway mapping in Windsurf

Cascade uses `kegg_link` and `kegg_get` to trace complex gene-to-pathway connections without manual input. It reads your codebase and pulls the exact biological data needed to verify your logic. You just define the target genes. Cascade handles the multi-step retrieval and presents the final, mapped pathway output directly in your editor.

Convert identifiers with KEGG inside Windsurf

Stop jumping between browser tabs to translate database IDs. This MCP Server lets Cascade use `kegg_conv` to map internal genomic IDs to KEGG standards on the fly. It keeps your workflow inside the IDE. Cascade identifies the mismatch, triggers the conversion tool, and applies the correct ID to your code instantly.

Automated drug interaction checks in Windsurf

Cascade runs `kegg_ddi` to flag potential adverse reactions for any compound set you define. It provides clear, actionable warnings before you commit your work. You gain immediate visibility into chemical interactions. Cascade fetches the data, compares it against your current project variables, and highlights risks in the editor.

Setup guide

Set up KEGG 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 KEGG 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 KEGG payment history." If connected, Cascade will call the KEGG tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

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

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by KEGG. 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 KEGG MCP in Windsurf

Use the `kegg_find` tool via the Cascade sidebar. Just ask your agent to search for a specific keyword or chemical identifier and it will return the matching entries.

Yes. The server pulls live data directly from the KEGG REST API. Your Windsurf session always accesses the most current database release information via `kegg_info`.

Absolutely. Just instruct Cascade to run `kegg_list` with the 'organism' parameter. It will fetch the full list of supported KEGG organisms for your analysis.

Your queries stay within your local Windsurf environment. This server only handles the specific biological identifiers you send to the KEGG API.

The server returns a standard error code. Cascade will report the failure in your chat panel, allowing you to refine your search parameters or check your connection.

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