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bio-mcp-evo2

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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

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