wetlab-mcp 0.1.0

A professional FastMCP server for in silico molecular biology and assay design

🧬 WetLab-MCP

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🔬 Overview

WetLab-MCP is a professional FastMCP server designed to bridge the gap between computational discovery and wet-lab execution. It provides a comprehensive suite of tools for qPCR primer design, cloning strategy optimization, and sequence specificity analysis, all integrated directly into your AI-assisted research workflow.

Starting with the industry-standard primer3-py engine, WetLab-MCP ensures deterministic, high-quality assay designs without ever needing an external API for core calculations.

🚀 Key Features

• design_qpcr_primers: Local, deterministic qPCR primer design enforcing standard $T_m$ and GC% constraints.
• design_cloning_primers: Intelligent cloning strategy with automatic restriction site detection and "junk" leader recommendations for high enzyme efficiency.
• design_taqman_probe: Automated TaqMan internal oligo design with industry-standard quenching rules (no 5' G).
• analyze_multiplex_compatibility: All-vs-all heterodimer analysis to detect cross-reactivity in multiplex PCR or panels.
• design_multi_gene_panel: Greedy optimization for building non-conflicting primer sets for multiple targets.
• check_primer_specificity: Live NCBI BLAST integration (blastn-short) to verify potential off-target binding.

🚀 Installation & Claude Integration

WetLab-MCP can be added to Claude Desktop using one of the following methods.

Method 1: Using uvx (Recommended)

This is the fastest way to run WetLab-MCP without manual installation. Ensure you have uv installed.

Add this to your claude_desktop_config.json:

{
  "mcpServers": {
    "WetLab-MCP": {
      "command": "uvx",
      "args": ["wetlab-mcp"]
    }
  }
}

Method 2: Using pip

If you prefer a standard installation:

pip install wetlab-mcp

Then add this to your claude_desktop_config.json:

{
  "mcpServers": {
    "WetLab-MCP": {
      "command": "python",
      "args": [
        "-m",
        "wetlab_mcp"
      ]
    }
  }
}

🧪 Tool Specifications

Tool	Purpose	Key Inputs
design_qpcr_primers	qPCR assays	Sequence, Target $T_m$
design_cloning_primers	Cloning/Gibson	Overhangs, Target $T_m$
design_taqman_probe	Real-time PCR	Sequence, Primers, Probe $T_m$
check_primer_specificity	Off-target check	Primer Sequence (Internet req.)
analyze_multiplex_compatibility	Dimer analysis	List of Primers
design_multi_gene_panel	Batch design	List of Genes ({name, seq})

🛡️ License

Distributed under the MIT License. See LICENSE for more information.

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Design by ZaEyAsa
Empowering Computational Biology with Agentic Precision