# 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
```bash
git clone https://github.com/bio-mcp/bio-mcp-evo2.git
cd bio-mcp-evo2
pip install -e .[dev]
```
### Container Installation
#### Docker
```bash
docker build -t bio-mcp-evo2 .
docker run --gpus all bio-mcp-evo2
```
#### Singularity (HPC)
```bash
singularity build --fakeroot evo2.sif Singularity.def
singularity run --nv evo2.sif
```
## Configuration
### Environment Variables
```bash
# 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`:
```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:
```json
{
"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.
```python
# 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.
```python
# Example usage
result = await evo2_score({
"sequence": "ATCGATCGATCGATCGATCG",
"return_logits": False
})
```
### evo2_embed
Extract learned representations from sequences.
```python
# Example usage
result = await evo2_embed({
"sequence": "ATCGATCGATCGATCGATCG",
"layer": "blocks.28.mlp.l3"
})
```
### evo2_variant_effect
Predict the effect of mutations.
```python
# 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.
```bash
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.
```bash
export BIO_MCP_EVO2_EXECUTION_MODE=local
python -m src.server
```
### SBATCH Mode
For HPC clusters with SLURM.
```bash
export BIO_MCP_EVO2_EXECUTION_MODE=sbatch
export BIO_MCP_EVO2_SBATCH_PARTITION=gpu
python -m src.server
```
### Container Modes
For isolated execution environments.
```bash
# 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
