How to Use the Ensembl MCP in Windsurf

Q: How do I install the Ensembl MCP Server in Windsurf?

Edit your /.codeium/windsurf/mcpconfig.json file. Add the server details under the mcpServers key, then click Refresh in the MCP panel. You can also use the built-in MCP Marketplace for a one-click setup.

Q: Can Windsurf chain Ensembl variant lookups automatically?

Yes. Cascade will chain getvariation to pull genotypes and population data, then immediately pass those results into getvepid for consequence prediction. You just ask for the final analysis.

Q: What happens if an Ensembl API endpoint fails in Windsurf?

The agent usually catches the error and runs ping to check if the service is alive. If the REST API is up, it checks getinforest for version mismatches and retries the request with corrected parameters.

Q: Does this integration support GA4GH beacon queries?

It does. You can instruct Cascade to run getga4ghbeacon to check for allele information. The agent can also use searchga4ghvariants if you need to search using the standard schema.

Let Windsurf's Cascade autonomously query Ensembl genomic data and write your bioinformatics pipelines.

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Connect Ensembl MCP to Windsurf

Create your Vinkius account to connect Ensembl 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 Ensembl with Windsurf

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Ensembl MCP Server bulk operations

Start a session by telling Cascade to analyze a batch of variants. The agent hits `get_vep_bulk` and pulls consequence predictions for multiple regions at once. If you need stable identifiers mapped, it chains `get_lookup_bulk` to find the species and database matches without you writing a single fetch request. That autonomous routing matters when dealing with large datasets. Cascade figures out the exact batch size, formats the payload, and parses the response directly into your workspace. You just watch the results populate in your editor.

Cross-reference and homology mapping

Genomic pipelines break when identifiers mismatch. You ask Windsurf to track down external symbols, and it runs `get_xrefs_symbol` to return the linked Ensembl objects. From there, the agent pivots to `get_homology` to pull related species data based on those gene IDs. You do not have to prompt each step. Cascade reads your initial intent, sees the missing links, and calls `get_taxonomy_id` if it needs taxonomic classifications to complete the script. The agent builds the multi-step context tree automatically.

Sequence extraction and alignment

Pulling raw sequences usually means scraping browser tabs. Don't do that. Your AI client uses `get_sequence_region` to grab exact genomic chunks based on coordinates. If you need alignments for that specific region, it fires `get_alignment` right after. It handles the coordinate conversions too. If you are starting with cDNA, Cascade runs `get_map_cdna` to get the genomic coordinates before pulling the sequence. The entire retrieval pipeline happens inline while you focus on the actual analysis logic.

Setup guide

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

mcp_config.json

{
  "mcpServers": {
    "ensembl-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 Ensembl. 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 Ensembl MCP in Windsurf

Edit your `~/.codeium/windsurf/mcp_config.json` file. Add the server details under the `mcpServers` key, then click Refresh in the MCP panel. You can also use the built-in MCP Marketplace for a one-click setup.

Yes. Cascade will chain `get_variation` to pull genotypes and population data, then immediately pass those results into `get_vep_id` for consequence prediction. You just ask for the final analysis.

The agent usually catches the error and runs `ping` to check if the service is alive. If the REST API is up, it checks `get_info_rest` for version mismatches and retries the request with corrected parameters.

It does. You can instruct Cascade to run `get_ga4gh_beacon` to check for allele information. The agent can also use `search_ga4gh_variants` if you need to search using the standard schema.

Your queries for allele frequencies and gene trees remain ephemeral. Windsurf routes requests directly to the endpoints via the MCP protocol. Vinkius isolates the execution environment, meaning your specific variant searches never persist on our infrastructure.

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