BioNeMo Framework

NVIDIA BioNeMo Framework is a is a comprehensive suite of programming tools, libraries, and models designed for computational drug discovery. It accelerates the most time-consuming and costly stages of building and adapting biomolecular AI models by providing domain-specific, optimized models and tooling that are easily integrated into GPU-based computational resources for the fastest performance on the market. You can access BioNeMo Framework as a free community resource here in this repository or learn more at https://www.nvidia.com/en-us/clara/bionemo/ about getting an enterprise license for improved expert-level support.

Structure of the Framework

The bionemo-framework is organized into independently installable namespace packages. These are located under the sub-packages/ directory. Please refer to PEP 420 – Implicit Namespace Packages for details.

Documentation Resources

• Official Documentation: For user guides, API references, and troubleshooting, visit our official documentation.
• In-Progress Documentation: To explore the latest features and developments, check the documentation reflecting the current state of the main branch here. Note that this may include references to features or APIs that are not yet finalized.

Getting Started with BioNeMo Framework

Full documentation on using the BioNeMo Framework is provided in our documentation: https://docs.nvidia.com/bionemo-framework/latest/user-guide/. To simplify the integration of optimized third-party dependencies, BioNeMo is primarily distributed as a containerized library. You can download the latest released container for the BioNeMo Framework from NGC. To launch a pre-built container, you can use the brev.dev launchable or execute the following command:

docker run --rm -it \
  --gpus=all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
  nvcr.io/nvidia/clara/bionemo-framework:nightly \
  /bin/bash

Setting up a local development environment

Initializing 3rd-party dependencies as git submodules

The NeMo and Megatron-LM dependencies are included as git submodules in bionemo2. The pinned commits for these submodules represent the "last-known-good" versions of these packages that are confirmed to be working with bionemo2 (and those that are tested in CI).

To initialize these sub-modules when cloning the repo, add the --recursive flag to the git clone command:

git clone --recursive git@github.com:NVIDIA/bionemo-framework.git
cd bionemo-framework

To download the pinned versions of these submodules within an existing git repository, run

git submodule update --init --recursive

Different branches of the repo can have different pinned versions of these third-party submodules. Ensure submodules are automatically updated after switching branches or pulling updates by configuring git with:

git config submodule.recurse true

NOTE: this setting will not download new or remove old submodules with the branch's changes. You will have to run the full git submodule update --init --recursive command in these situations.

Build the Docker Image Locally

With a locally cloned repository and initialized submodules, build the BioNeMo container using:

docker buildx build . -t my-container-tag

VSCode Devcontainer for Interactive Debugging

We distribute a development container configuration for vscode (.devcontainer/devcontainer.json) that simplifies the process of local testing and development. Opening the bionemo-framework folder with VSCode should prompt you to re-open the folder inside the devcontainer environment.

Note

The first time you launch the devcontainer, it may take a long time to build the image. Building the image locally (using the command shown above) will ensure that most of the layers are present in the local docker cache.

Quick Start

See the tutorials pages for example applications and getting started guides.