# LynxKite Bio

An expansion for `lynxkite-graph-analytics` that provides tools for biological applications.

# Installation

```
pip install lynxkite-bio
```

After installing `lynxkite-bio`, LynxKite should automatically detect it and make the new operations available.

## BioNeMo

BioNeMo can be used two ways:

- For ESM-2, Evo 2, and Geneformer you can run LynxKite inside a BioNeMo Docker image that contains these models.
- Other BioNeMo models are run as NIMs and LynxKite can communicate with them over HTTP.

### Docker image

To build the image:

```bash
# in lynxkite-graph-analytics folder
$ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
$ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo
```

If you want to do some development, then it is recommended to use the [devcontainers](https://code.visualstudio.com/docs/devcontainers/containers)
VS Code extension. The following is a basic configuration to get started:

```json
// .devcontainer/devcontainer.json
{
	"name": "Existing Dockerfile",
	"runArgs": [
		"--gpus=all",
		"--shm-size=4g"
	],
	"build": {
		"context": "..",
		"dockerfile": "../lynxkite-bio/Dockerfile.bionemo"
	}
}
```