bio-mcp-evo2 by bio-mcp - MCP Server

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