Heor Agent MCP vs Encode Toolkit

In-depth architectural comparison of the Heor Agent MCP and Encode Toolkit MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Heor Agent MCP when:

• You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: literature_search, screen_abstracts, risk_of_bias.

Explore Heor Agent MCP Details

Choose Encode Toolkit when:

• You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: encode_search_experiments, encode_get_experiment, encode_download_files.

Explore Encode Toolkit Details

Feature & Specification Comparison

Specification	Heor Agent MCP neptun2000 Biology, Medicine and Bioinformatics	Encode Toolkit ammawla Biology, Medicine and Bioinformatics
Summary	HEOR (Health Economics and Outcomes Research) MCP server with 7 tools for literature search across 41 medical data sources (PubMed, NICE, CADTH, ICER, etc.), cost-effectiveness modeling (Markov/PartSA/PSA), and HTA dossier preparation for pharmaceutical and biotech teams.	MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments.
Category & Scope

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "neptun2000-heor-agent-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "heor-agent-mcp"
      ]
    }
  }
}

{
  "mcpServers": {
    "ammawla-encode-toolkit": {
      "command": "uvx",
      "args": [
        "encode-toolkit"
      ]
    }
  }
}

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