lynxkite-bio/README.md

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:

# 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 VS Code extension. The following is a basic configuration to get started:

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