BioNeMo Framework

What is BioNeMo Framework?

BioNeMo Framework provides versatile functionalities for developing, training and deploying large language models. BioNeMo allows users to build biomolecular models by providing access to pre-trained models, creating workflows to fit downstream task models from embeddings, and generating biomolecules that meet user-specified criteria based on the fit model. Built for supercomputing scale, the framework allows developers to easily configure and deploy distributed multi-node jobs with minimal code.

This container contains implementation of the following models :

• DNABERT
• OpenFold
• MolMIM
• EquiDock
• DiffDock
• ESM-2nv
• ESM-1nv
• ProtT5
• MegaMolBART

This container also supports downstream tasks like Protein secondary structure prediction, Protein thermostability using Meltome Atlas, Subcellular localization, Retrosynthesis and fine-tuning on FLIP /PhysChem datasets.

Getting Started With BioNeMo Framework

For information about how to get started with BioNeMo refer to the documentation

Compatible Infrastructure Software Versions

BioNeMo is only supported on x86 Linux systems. If you are not on such a system, you must use the project's Docker images to develop and execute BioNeMo code.

System Requirements:

• Docker (with GPU support, docker engine >= 19.03).
• Ubuntu 20.04 or Higher
• NVIDIA GPU, if you intend to do model training. BioNeMo is compatible with most NVIDIA GPUs, with some incompatibility: Tested GPUs:
  • DGX-H100, A100, V100
  • RTX A6000, A8000
  • Tesla T4
  • GeForce RTX 2080 Ti
• GPUs with known issues:
  • Tesla K80
• bfloat16 precision requires an Ampere generation GPU or higher.

Security Vulnerabilities in Open Source Packages

BioNeMo Framework v24.03 container is vulnerable to GHSA-whh8-fjgc-qp73 in onnx 1.14.0. Users are advised not to open untrusted onnx files with this image. Restrict your mount point to minimize directory traversal impact

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License

This container is licensed under the NVIDIA AI Product AgreementBy pulling and using this container, you accept the terms and conditions of this license. By pulling and using the container, you accept the terms and conditions of the