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@rezashamji rezashamji commented Jan 6, 2026

This PR adds ESM-C (Evolutionary Scale Modeling) as a remote, MCP-native tool in ToolUniverse, following the recommended remote tool onboarding pattern for models without an existing public API.

Model
ESM-C (from EvolutionaryScale / CZI Biohub)
GitHub: https://github.com/evolutionaryscale/esm

What this PR does

  • Implements a lightweight FastMCP server that wraps ESM-C inference and exposes a single MCP tool:

    • esm_embed_sequence — generates protein sequence embeddings using ESM-C.
  • Adds an MCPAutoLoaderTool configuration (esm_remote.json) so ToolUniverse can automatically discover and invoke the tool via MCP.

  • Keeps all model execution fully remote, with no ESM or GPU dependencies required on the ToolUniverse client side.

Why this matters

  • Unblocks onboarding of Biohub / CZI models that do not yet have public APIs, by providing a clean, agent-native interface layer.
  • Enables hosted deployment (e.g., Biohub / CZI GPU infrastructure) as well as local or private deployment by external users.
  • Establishes a reusable template for bringing current and future Biohub / Virtual Cell Platform models into ToolUniverse without requiring immediate REST API productization.

This aligns with the broader goal of making Biohub / CZI models directly usable inside ToolUniverse’s AI-scientist workflows while preserving flexibility around hosting, security, and future API evolution.

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