What is the key difference between Encode Toolkit and Decoder 3am MCP?

Encode Toolkit belongs to the Biology, Medicine and Bioinformatics category with local stdio execution, while Decoder 3am MCP belongs to the Biology, Medicine and Bioinformatics category with local stdio execution.

How do I install Encode Toolkit or Decoder 3am MCP in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Encode Toolkit and Decoder 3am MCP free or paid?

Encode Toolkit operates under a Free / Open Source model (No auth required). Decoder 3am MCP operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Encode Toolkit lists 20 tools with 3 views and 24 GitHub stars. Decoder 3am MCP lists 4 tools with 3 views and 1 GitHub stars.

Can I use both Encode Toolkit and Decoder 3am MCP together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Encode Toolkit vs Decoder 3am MCP

In-depth architectural comparison of the Encode Toolkit and Decoder 3am MCP 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.

At a Glance & Executive Verdict

Encode Toolkit

Biology, Medicine and Bioinformatics · Local stdio

Quality: 57/100 (Good) | Auth: No auth required

Decoder 3am MCP

Biology, Medicine and Bioinformatics · Local stdio

Quality: 45/100 (Fair) | Auth: No auth required

Verdict Summary: Choose Encode Toolkit if you need specialized Biology, Medicine and Bioinformatics tools running via a local process. Choose Decoder 3am MCP if your workspace requires Biology, Medicine and Bioinformatics integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

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

Choose Decoder 3am 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: classify_sleep_cause, get_cause_info, list_causes.

Explore Decoder 3am MCP Details

Feature & Specification Comparison

Specification	Encode Toolkit ammawla Biology, Medicine and Bioinformatics	Decoder 3am MCP thelongevityvault Biology, Medicine and Bioinformatics
Summary	MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments.	Sleep disruption cause classifier using The Longevity Vault's 5-cause framework. Identifies the biological mechanism behind 3am wakeups from symptom descriptions, with tracked links to the full interactive 3AM Decoder.
Category & Scope

Tools & Capabilities Breakdown

Encode Toolkit Tools (20)

encode_search_experiments

Search ENCODE experiments with 20+ filters.

encode_get_experiment

Get full details for a single experiment including all files, quality metrics, and audit info.

encode_download_files

Download specific files by accession to a local directory.

encode_batch_download

Search + download in one step. Runs in preview mode by default.

encode_track_experiment

Track an experiment locally with its publications, methods, and pipeline info.

encode_list_files

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).

Encode Toolkit Configuration

mcpServers (Claude Desktop / Cursor)

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

Decoder 3am MCP Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "thelongevityvault-decoder-3am-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "thelongevityvault-decoder-3am-mcp"
      ]
    }
  }
}

Frequently Asked Questions

Encode Toolkit is categorized under Biology, Medicine and Bioinformatics and uses a local stdio subprocess. In contrast, Decoder 3am MCP belongs to Biology, Medicine and Bioinformatics using local stdio subprocess. Select Encode Toolkit when you need capabilities focused on biology, medicine and bioinformatics and Decoder 3am MCP when you require tools for biology, medicine and bioinformatics.

More alternatives to Encode Toolkit More alternatives to Decoder 3am MCP Biology, Medicine and Bioinformatics category hub