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Third-Party Notices

BioNeMo Inference Runtime (BioIR) uses the third-party software listed below. Each component remains governed by its own license. The Apache License 2.0 for NVIDIA-authored BioIR code does not replace those terms.

Dependency constraints remain authoritative in the project manifests. The release SBOM records the resolved dependency versions. This notice records a version or revision only when it identifies source copied into BioIR, code compiled into a distributed artifact, or a pinned reference submodule.

The root LICENSE contains Apache-2.0. Other reusable license texts are under LICENSES/. Component-specific license and notice files distributed by an upstream package remain authoritative for that package.

Distributed Source and Derived Code

  • OpenFold and AlphaFold source excerpts

    • Version: source excerpts; no upstream release pin
    • Copyright: AlQuraishi Laboratory and DeepMind Technologies Limited
    • License: Apache-2.0; see LICENSE
    • Source: OpenFold and AlphaFold
    • Distribution: adapted files ship in the public source tree and wheel
    • Modifications: integration with BioIR data structures, optimized layers, checkpoint conversion, and output handling

  • Ray source excerpt

    • Version: Ray 2.53.0 source excerpt
    • Copyright: Ray Authors
    • License: Apache-2.0; see LICENSE
    • Source: Ray pipeline stage
    • Distribution: adapted code ships in bionemo_ir/pipeline/stages/base.py

  • vLLM source excerpt

    • Version: source excerpt; no upstream release pin
    • Copyright: vLLM contributors
    • License: Apache-2.0; see LICENSE
    • Source: vLLM
    • Distribution: adapted code ships in bionemo_ir/dsl_kernels/triton/fused_swiglu.py

  • PyTorch3D source excerpt

    • Version: source excerpt; no upstream release pin
    • Copyright: Meta Platforms, Inc. and affiliates
    • License: BSD-3-Clause; see LICENSES/BSD-3-Clause.txt
    • Source: PyTorch3D
    • Distribution: copied code ships in bionemo_ir/_torch/layers/random_augmentation.py; adapted arithmetic also ships in bionemo_ir/dsl_kernels/triton/quaternion_rotation.py

  • Quack source excerpt

    • Version: source excerpt; no upstream release pin
    • Copyright: Wentao Guo, Ted Zadouri, and Tri Dao
    • License: Apache-2.0; see LICENSE
    • Source: Quack cache implementation
    • Distribution: adapted code ships in bionemo_ir/dsl_kernels/cute_cache.py

  • cuEquivariance source excerpt

    • Version: source excerpt from the cuEquivariance implementation
    • Copyright: NVIDIA Corporation and affiliates
    • License: Apache-2.0; see LICENSE
    • Source: cuEquivariance
    • Distribution: adapted code ships in bionemo_ir/dsl_kernels/triton/fused_ln_proj_moveaxis_pad.py

  • CUTLASS-derived CuTe DSL source

    • Version: source excerpts associated with nvidia-cutlass-dsl 4.5.2
    • Copyright: NVIDIA Corporation and affiliates
    • License: BSD-3-Clause or NVIDIA Software License, as marked per source file
    • Source: CUTLASS and CuTe DSL license
    • Distribution: BSD-3-Clause files may ship; proprietary CuTe DSL source is removed from public artifacts before release

  • TensorRT-LLM source excerpt

    • Version: source excerpt; no upstream release pin
    • Copyright: NVIDIA Corporation and affiliates
    • License: Apache-2.0; see LICENSE
    • Source: TensorRT-LLM
    • Distribution: adapted layout code ships in bionemo_ir/_torch/layers/linear.py

Compiled into BioIR

  • nanobind
    • Version: 2.10.2
    • Copyright: Wenzel Jakob and contributors
    • License: BSD-3-Clause; see LICENSES/BSD-3-Clause.txt
    • Source and license: nanobind 2.10.2
    • Distribution: statically compiled into BioIR extension modules
    • Modifications: none

Runtime Dependencies

These direct runtime dependencies are downloaded separately by the recipient's package installer and are not included in the BioIR source distribution or wheel. Their package-provided license and notice files remain authoritative.

  • apache-tvm-ffi

  • torch

    • Copyright: PyTorch contributors
    • License: compound upstream license bundle, including Apache-2.0, BSD-2-Clause, BSD-3-Clause, BSL-1.0, MIT, and LLVM exceptions
    • Source and license: PyTorch
    • Notice: preserve the LICENSE, NOTICE, and third-party license files from the installed distribution

  • cuequivariance

    • Copyright: NVIDIA Corporation and affiliates
    • License: Apache-2.0; see LICENSE
    • Source and license: cuEquivariance

  • nvidia-cudnn-frontend

  • triton

  • biopython

  • ray

    • Copyright: Ray Authors
    • License: Apache-2.0; see LICENSE
    • Source and license: Ray

  • uvloop

    • Copyright: MagicStack Inc. and uvloop contributors
    • License: MIT OR Apache-2.0; BioIR records the MIT option
    • License: LICENSES/MIT.txt
    • Source: uvloop

  • modelcif

  • rdkit

  • biotite

  • datasets

    • Copyright: Hugging Face and contributors
    • License: Apache-2.0; see LICENSE
    • Source and license: Datasets

  • huggingface-hub

  • PyYAML

  • lru-dict

  • kalign-python

    • Copyright: Timo Lassmann and contributors
    • License: Apache-2.0; see LICENSE
    • Source and license: Kalign

  • scipy

    • Copyright: SciPy developers
    • License: BSD-3-Clause with bundled third-party notices
    • Source and license: SciPy
    • Notice: preserve the package-provided license bundle from the installed distribution

  • gemmi

    • Copyright: Global Phasing Ltd.
    • License: MPL-2.0 OR LGPL-3.0-or-later; BioIR records the MPL-2.0 option
    • License: LICENSES/MPL-2.0.txt
    • Source: Gemmi
    • Distribution: obtained independently by recipients; not included in the BioIR source distribution or wheel

  • einops

  • pydantic

NVIDIA-Licensed Runtime Dependencies

These NVIDIA packages are included in the component inventory but are not third-party OSS. Their package-specific NVIDIA terms control their use and distribution.

  • cuda-python — LicenseRef-NVIDIA-SOFTWARE-LICENSE; package and terms
  • cuequivariance-ops-cu13 — LicenseRef-NVIDIA-MATH-LIBRARIES-SDK; package
  • cuequivariance-ops-torch-cu13 — LicenseRef-NVIDIA-MATH-LIBRARIES-SDK; package
  • nvidia-cutlass-dsl — LicenseRef-NVIDIA-SOFTWARE-LICENSE; package and terms

Reference Submodules

The following pinned submodules support parity and reference tests. They do not ship in the BioIR wheel or runtime container.

  • OpenFold3

    • Commit: 0bb17be5199846e806b6347b6e17c6249c88ff1b
    • Copyright: AlQuraishi Laboratory and contributors
    • License: Apache-2.0; see LICENSE
    • Source and license: OpenFold3 commit

  • Protenix

    • Commit: 2475421477ab414b571149ad4a875c390ff8a35d
    • Copyright: ByteDance and Protenix contributors
    • License: Apache-2.0; see LICENSE
    • Source and license: Protenix commit

Build and Development Dependencies

These tools are used to build or test BioIR. They do not ship in the wheel or runtime container unless an artifact-specific SBOM states otherwise.

Base Images

  • NVIDIA PyTorch container — selected in docker/Dockerfile; used only for build and development stages
  • NVIDIA CUDA container — selected in docker/Dockerfile; used when a recipient builds the runtime image

The image-provided OSS notices and license files must remain in derivative images. The release SBOM, rather than this repository inventory, records the resolved operating-system and base-image package closure.