MCP Setup¶

AIVA exposes a Model Context Protocol (MCP) server that allows MCP-compatible clients such as Claude Desktop to access AIVA's genomic analysis tools directly.

MCP Endpoint¶

https://api.aivaportal.com/mcp/sse

The MCP server uses Server-Sent Events (SSE) transport for real-time communication.

Claude Desktop Configuration¶

To connect AIVA to Claude Desktop, add the following configuration to your Claude Desktop settings file.

Configuration File Location¶

Platform	Path
macOS	`~/Library/Application Support/Claude/claude_desktop_config.json`
Windows	`%APPDATA%\Claude\claude_desktop_config.json`

Configuration¶

Add the AIVA MCP server to the mcpServers section of your configuration file:

{
  "mcpServers": {
    "aiva": {
      "url": "https://api.aivaportal.com/mcp/sse",
      "headers": {
        "Authorization": "Bearer <AIVA_API_KEY>"
      }
    }
  }
}

Replace <AIVA_API_KEY> with your actual API key. See API Keys for instructions on creating a key.

After updating the configuration, restart Claude Desktop for the changes to take effect.

Available Tools¶

Once connected, the following AIVA tools become available in your MCP client:

Tool	Description
`postgresql`	Query your uploaded variant data using SQL
`web_search`	Search the web for genomic and biomedical information
`variant_annotation`	Annotate variants with ClinVar, gnomAD, CADD, SIFT, PolyPhen
`pubtator`	Search biomedical literature databases
`python_repl`	Execute Python code for data analysis and visualization
`knowledge_graph`	Query the gene-protein-drug interaction network
`clinical_trials`	Search clinical trials databases
`phen2gene`	Phenotype-to-gene prioritization

Example Prompts¶

Once AIVA is connected as an MCP server, you can use prompts like these in Claude Desktop:

Querying variant data:

"Query my patient_001_variants table and find all pathogenic variants in BRCA1 and BRCA2 genes."

Variant annotation:

"Annotate the variant chr17:41245466 G>A and tell me about its clinical significance."

Literature search:

"Search PubMed for recent publications about CFTR variants and cystic fibrosis treatment."

Data analysis:

"Analyze the variant distribution by chromosome in my sample and create a bar chart."

Knowledge graph:

"What drugs target the protein encoded by the EGFR gene?"

Clinical trials:

"Find active clinical trials for BRCA1-positive breast cancer patients."

Troubleshooting¶

Connection Issues¶

Verify your API key is valid by using the health check endpoint.
Ensure the configuration JSON is valid (no trailing commas, correct quoting).
Restart Claude Desktop after making configuration changes.

Tool Access¶

Tools are available based on your subscription tier.
Ensure you have at least one uploaded sample if you want to query variant data.

Authentication Errors¶

API keys are case-sensitive. Copy the key exactly as shown at creation time.
If a key has expired or been revoked, create a new one from Settings > API Keys in the AIVA application.