bio-mcp-evo2

MCP server for evo2 DNA language model - enabling AI assistants to generate and analyze DNA sequences using state-of-the-art genomic foundation models.

Overview

evo2 is a genomic foundation model capable of:

• Generating DNA sequences with specified properties
• Scoring sequence likelihoods and calculating perplexity
• Extracting learned representations for downstream tasks
• Predicting variant effects on biological function

This MCP server provides multiple execution modes to support various computational environments:

• Local: Direct GPU execution (requires H100 or compatible GPU)
• SBATCH: Submit jobs to SLURM clusters
• Singularity/Docker: Container-based execution
• API: Nvidia NIM cloud API (no local GPU required)

Installation

Local Installation

git clone https://github.com/bio-mcp/bio-mcp-evo2.git
cd bio-mcp-evo2
pip install -e .[dev]

Container Installation

Docker

docker build -t bio-mcp-evo2 .
docker run --gpus all bio-mcp-evo2

Singularity (HPC)

singularity build --fakeroot evo2.sif Singularity.def
singularity run --nv evo2.sif

Configuration

Environment Variables

# Execution mode selection
export BIO_MCP_EVO2_EXECUTION_MODE=api  # Options: local, sbatch, singularity, docker, api

# Model configuration
export BIO_MCP_EVO2_MODEL_SIZE=7b  # Options: 7b, 40b
export BIO_MCP_EVO2_CUDA_DEVICE=0

# API configuration (for API mode)
export BIO_MCP_EVO2_NIM_API_KEY=your-api-key

# SBATCH configuration (for HPC clusters)
export BIO_MCP_EVO2_SBATCH_PARTITION=gpu
export BIO_MCP_EVO2_SBATCH_TIME=01:00:00
export BIO_MCP_EVO2_SBATCH_MEMORY=64G
export BIO_MCP_EVO2_SBATCH_GPU_TYPE=h100

Claude Desktop Integration

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "bio-evo2": {
      "command": "python",
      "args": ["-m", "src.server"],
      "cwd": "/path/to/bio-mcp-evo2",
      "env": {
        "BIO_MCP_EVO2_EXECUTION_MODE": "api",
        "BIO_MCP_EVO2_NIM_API_KEY": "your-api-key"
      }
    }
  }
}

For HPC with Singularity:

{
  "mcpServers": {
    "bio-evo2": {
      "command": "singularity",
      "args": ["run", "--nv", "/path/to/evo2.sif"],
      "env": {
        "BIO_MCP_EVO2_EXECUTION_MODE": "local"
      }
    }
  }
}

Available Tools

evo2_generate

Generate DNA sequences from a prompt.

# Example usage
result = await evo2_generate({
    "prompt": "ATCGATCGATCG",
    "n_tokens": 100,
    "temperature": 1.0,
    "top_k": 4
})

evo2_score

Calculate sequence perplexity or get raw logits.

# Example usage
result = await evo2_score({
    "sequence": "ATCGATCGATCGATCGATCG",
    "return_logits": False
})

evo2_embed

Extract learned representations from sequences.

# Example usage
result = await evo2_embed({
    "sequence": "ATCGATCGATCGATCGATCG",
    "layer": "blocks.28.mlp.l3"
})

evo2_variant_effect

Predict the effect of mutations.

# Example usage
result = await evo2_variant_effect({
    "reference_sequence": "ATCGATCGATCGATCGATCG",
    "variant_sequence": "ATCGATCGATCGATCAATCG",
    "context_window": 1000
})

Execution Modes

API Mode (Recommended for Getting Started)

No GPU required. Uses Nvidia's hosted API.

export BIO_MCP_EVO2_EXECUTION_MODE=api
export BIO_MCP_EVO2_NIM_API_KEY=your-key
python -m src.server

Local Mode

Requires H100 GPU with sufficient memory.

export BIO_MCP_EVO2_EXECUTION_MODE=local
python -m src.server

SBATCH Mode

For HPC clusters with SLURM.

export BIO_MCP_EVO2_EXECUTION_MODE=sbatch
export BIO_MCP_EVO2_SBATCH_PARTITION=gpu
python -m src.server

Container Modes

For isolated execution environments.

# Docker
export BIO_MCP_EVO2_EXECUTION_MODE=docker
docker run --gpus all -v $PWD:/workspace bio-mcp-evo2

# Singularity
export BIO_MCP_EVO2_EXECUTION_MODE=singularity
singularity run --nv evo2.sif

Examples

Generate a promoter sequence

User: Generate a 200bp DNA sequence that could function as a promoter