{"id":17980816,"url":"https://github.com/nvidia/bionemo-framework","last_synced_at":"2025-04-14T19:47:54.079Z","repository":{"id":259334399,"uuid":"705428944","full_name":"NVIDIA/bionemo-framework","owner":"NVIDIA","description":"BioNeMo Framework: For building and adapting AI models in drug discovery at scale","archived":false,"fork":false,"pushed_at":"2025-04-14T16:41:36.000Z","size":249641,"stargazers_count":388,"open_issues_count":104,"forks_count":64,"subscribers_count":41,"default_branch":"main","last_synced_at":"2025-04-14T17:31:36.004Z","etag":null,"topics":["drug-discovery","gpu","machine-learning","pytorch"],"latest_commit_sha":null,"homepage":"https://nvidia.github.io/bionemo-framework/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NVIDIA.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE/license.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":"CODEOWNERS","security":"SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-10-16T01:31:06.000Z","updated_at":"2025-04-14T00:45:09.000Z","dependencies_parsed_at":"2024-12-13T19:41:52.889Z","dependency_job_id":"ca7a0de5-d4b1-4a06-b9f5-e112387dc034","html_url":"https://github.com/NVIDIA/bionemo-framework","commit_stats":null,"previous_names":["nvidia/bionemo-framework"],"tags_count":12,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NVIDIA%2Fbionemo-framework","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NVIDIA%2Fbionemo-framework/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NVIDIA%2Fbionemo-framework/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NVIDIA%2Fbionemo-framework/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NVIDIA","download_url":"https://codeload.github.com/NVIDIA/bionemo-framework/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248951160,"owners_count":21188410,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["drug-discovery","gpu","machine-learning","pytorch"],"created_at":"2024-10-29T18:06:28.397Z","updated_at":"2025-04-14T19:47:54.070Z","avatar_url":"https://github.com/NVIDIA.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioNeMo Framework\n\n[![Click here to deploy.](https://uohmivykqgnnbiouffke.supabase.co/storage/v1/object/public/landingpage/brevdeploynavy.svg)](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU)\n[![Docs Build](https://img.shields.io/github/actions/workflow/status/NVIDIA/bionemo-framework/pages/pages-build-deployment?label=docs-build)](https://nvidia.github.io/bionemo-framework)\n[![Test Status](https://github.com/NVIDIA/bionemo-framework/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/NVIDIA/bionemo-framework/actions/workflows/unit-tests.yml)\n[![Latest Tag](https://img.shields.io/github/v/tag/NVIDIA/bionemo-framework?label=latest-version)](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework/tags)\n[![codecov](https://codecov.io/gh/NVIDIA/bionemo-framework/branch/main/graph/badge.svg?token=XqhegdZRqB)](https://codecov.io/gh/NVIDIA/bionemo-framework)\n\nNVIDIA BioNeMo Framework is a is a comprehensive suite of programming tools, libraries, and models designed for computational drug discovery.\nIt accelerates the most time-consuming and costly stages of building and adapting biomolecular AI models by providing\ndomain-specific, optimized models and tooling that are easily integrated into GPU-based computational resources for the\nfastest performance on the market. You can access BioNeMo Framework as a free community resource here in this repository\nor learn more at \u003chttps://www.nvidia.com/en-us/clara/bionemo/\u003e about getting an enterprise license for improved\nexpert-level support.\n\nBioNeMo Framework is part of a larger ecosystem of NVIDIA Biopharma products. Get notified of new releases, bug fixes, critical security updates, and more for biopharma. [Subscribe.](https://www.nvidia.com/en-us/clara/biopharma/product-updates/)\n\n## Structure of the Framework\n\nThe `bionemo-framework` is organized into independently installable namespace packages. These are located under the\n`sub-packages/` directory. Please refer to [PEP 420 – Implicit Namespace Packages](https://peps.python.org/pep-0420/)\nfor details.\n\n\n## Documentation Resources\n\n- **Official Documentation:** For user guides, API references, and troubleshooting, visit our [official documentation](https://docs.nvidia.com/bionemo-framework/latest/).\n- **In-Progress Documentation:** To explore the latest features and developments, check the documentation reflecting the current state of the `main` branch [here](https://nvidia.github.io/bionemo-framework/). Note that this may include references to features or APIs that are not yet finalized.\n\n## Getting Started with BioNeMo Framework\n\nFull documentation on using the BioNeMo Framework is provided in our documentation:\n\u003chttps://docs.nvidia.com/bionemo-framework/latest/user-guide/\u003e. 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\n[NGC](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework). To launch a pre-built container, you can use the brev.dev launchable [![ Click here to deploy.](https://uohmivykqgnnbiouffke.supabase.co/storage/v1/object/public/landingpage/brevdeploynavy.svg)](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU) or execute the following command:\n\n```bash\ndocker run --rm -it \\\n  --gpus=all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \\\n  nvcr.io/nvidia/clara/bionemo-framework:nightly \\\n  /bin/bash\n```\n\n### Setting up a local development environment\n\n#### Initializing 3rd-party dependencies as git submodules\n\nThe 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\nthat are confirmed to be working with bionemo2 (and those that are tested in CI).\n\nTo initialize these sub-modules when cloning the repo, add the `--recursive` flag to the git clone command:\n\n```bash\ngit clone --recursive git@github.com:NVIDIA/bionemo-framework.git\ncd bionemo-framework\n```\n\nTo download the pinned versions of these submodules within an existing git repository, run\n\n```bash\ngit submodule update --init --recursive\n```\n\nDifferent 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:\n\n\n```bash\ngit config submodule.recurse true\n```\n\n**NOTE**: this setting will not download **new** or remove **old** submodules with the branch's changes.\nYou will have to run the full `git submodule update --init --recursive` command in these situations.\n\n#### Build the Docker Image Locally\n\n\nWith a locally cloned repository and initialized submodules, build the BioNeMo container using:\n\n```bash\ndocker buildx build . -t my-container-tag\n```\n\n\n#### VSCode Devcontainer for Interactive Debugging\n\nWe distribute a [development container](https://devcontainers.github.io/) configuration for vscode\n(`.devcontainer/devcontainer.json`) that simplifies the process of local testing and development. Opening the\nbionemo-framework folder with VSCode should prompt you to re-open the folder inside the devcontainer environment.\n\n\u003e [!NOTE]\n\u003e The first time you launch the devcontainer, it may take a long time to build the image. Building the image locally\n\u003e (using the command shown above) will ensure that most of the layers are present in the local docker cache.\n\n### Quick Start\n\nSee the [tutorials pages](https://docs.nvidia.com/bionemo-framework/latest/user-guide/examples/bionemo-esm2/pretrain/)\nfor example applications and getting started guides.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvidia%2Fbionemo-framework","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnvidia%2Fbionemo-framework","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvidia%2Fbionemo-framework/lists"}