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Documentation Index

Fetch the complete documentation index at: https://docs.synthesize.bio/llms.txt

Use this file to discover all available pages before exploring further.

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Overview

Synthesize Bio MCP lets an AI tool send a structured request to Synthesize Bio, wait for the analysis to finish, and return the finished result to the user.

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What it analyzes

The MCP is built for differential gene expression workflows driven by natural-language prompts. A typical request compares two groups, such as:
  • heart vs liver
  • tumor vs normal tissue
  • CD4+ T cells vs CD8+ T cells

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What Claude does behind the scenes

Each analysis runs as a multi-step workflow:
  1. Claude submits the request to Synthesize Bio.
  2. Synthesize Bio extracts the sample groups described in the prompt.
  3. The platform runs gene expression model inference.
  4. The platform performs statistical differential expression analysis.
  5. Claude returns the completed output when the workflow finishes.

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What to expect from results

  • Most analyses take about 3 to 5 minutes.
  • Claude may show progress updates while the job is still running.
  • Completed results can include a readable report plus a JSON artifact for full technical details.

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Current limits

  • The workflow performs one pairwise comparison at a time.
  • If your prompt implies more than two groups, the current behavior compares the first two groups alphabetically.
  • The statistical testing step uses Welch’s t-test with Benjamini-Hochberg correction.
For setup instructions, continue to Set up the Claude Connector.