Evidence Methods / method

Containerized GPU runtime and viewer-state lane

NVIDIA Container Toolkit install/docker-specialized docs and Docker run/Compose GPU guidance now pair with Buildx build/imagetools, build/SBOM/GitHub Actions attestations, Compose build-spec and annotation metadata docs, plus Nextflow/Snakemake container reproducibility guidance, MMseqs2/Foldseek operational references, Apptainer Docker/OCI and admin-install material, OpenMM/OpenMMTools/OpenFE protocol docs, MDAnalysis trajectory transforms, Gemmi CIF/model docs, and Singularity GPU/data-container references to define a clearer containerized execution lane.

Evidence MethodsMethod

GPU container runtime docs and viewer-plugin references now tighten reproducibility for interactive molecular workflows

This makes runtime assumptions explicit when moving from local experiments to portable container workflows across GPU and HPC-style environments.

NVIDIA CTK NVIDIA CTK Docker docker run --gpus Docker BuildKit Build Cache Backends docker buildx bake Dockerfile Reference docker buildx build imagetools create Build Checks Build Check Rules Build Policies docker scout cves docker scout compare docker scout sbom Scout SBOM How-To Scout Policy docker scout policy docker scout quickview scout recommendations Scout Policy View Scout Remediation Build Secrets Cache Invalidate Multi-stage Builds SLSA Provenance Build Attestations SBOM Attestations GHA Attestations Compose Build Spec Build Annotations Docker Cache GHA Docker CI Cache Compose GPU Nextflow Containers Snakemake Deploy Apptainer OCI apptainer oci CLI Apptainer Fakeroot Apptainer Build apptainer build CLI apptainer cfg fakeroot Apptainer OCI Runtime Apptainer Registry Apptainer GPU Singularity GPU Apptainer Binds Apptainer Cgroups Apptainer Overlays Apptainer Install Singularity Data BioContainers micromamba Docker NCBI datasets CLI Mol* Instance Mol* Display Mol* Selections Mol* Integrations Mol* Query Params Mol* Quick Styles Mol* URL Tips Mol* Viewport Mol* Measurements MolViewSpec USD API Front Blender 4.3 Py API Blender 4.4 Py API Blender 4.5 Py API Blender 5.0 Py API Blender 5.1 Py API Blender 5.2 Py API Blender Extensions OpenMM Cookbook OpenMM Start OpenMM Alchemical OpenMMTools Docs OpenMMTools Start OpenFE Docs OpenFE RBFE CLI OpenFE Protocols MDAnalysis Transforms MDAnalysis Align MDAnalysis Contacts MDAnalysis H-Bonds MDTraj RMSD MDTraj Contacts MDTraj Distances MDTraj H-Bonds Gemmi CIF Gemmi Mol Models MMseqs2 Wiki Foldseek Wiki Simulation Zone Repeat Zone For Each Zone GN Tool Nodes GN Baking Biopython Pairwise Biopython SeqIO Biopython AlignIO USD Ar Hydra 2.0 Start Hydra 2.0 Dev USD Variants USD Layer Refs USD Shading Tut Hydra Scene Browser Hydra Framework UsdRender UsdShade UsdMtlx UsdGeom UsdLux UsdVol UsdSkel UsdRi UsdMedia UsdProc Sdf Foundations USD Glossary ChimeraX User Guide ChimeraX usage ChimeraX hbonds ChimeraX select ChimeraX measure ChimeraX distance Biotite Structure Biotite RMSD Biotite Superimpose Blender glTF

Key points

NVIDIA Toolkit install + docker-specialized docs, docker run/Compose GPU guidance, Buildx build/imagetools, build checks/rule references, build-input policy validation docs, build secrets/cache-invalidation/multi-stage references, SLSA provenance guidance, and build/SBOM/GHA attestations define host/runtime prerequisites plus supply-chain metadata behavior.

Scout cves/compare/sbom references, SBOM how-to guidance, policy dashboard + CLI docs, quickview/recommendations command references, and policy-view/remediation guidance complement build checks and policy validation so image governance can be inspected from both pipeline and artifact perspectives.

Compose build-spec plus annotation docs, alongside Nextflow/Snakemake container deployment references and micromamba-docker guidance, make workflow-level reproducibility controls and orchestration assumptions easier to audit.

Apptainer and Singularity GPU/bind/data-container docs plus admin-install guidance expose execution mechanics common in cluster and HPC environments, including OCI-to-SIF portability routes and fakeroot operating modes.

OpenUSD core + schema pages (UsdGeom/UsdLux/UsdVol/UsdMtlx/UsdSkel/UsdRi/UsdMedia/UsdProc/Sdf/Hydra) plus authoring-variants tutorial docs, Mol* display/selection/state + viewport + measurements docs, ChimeraX user/usage/select/measure/distance command pages, Biotite structure/RMSD/superimpose APIs, Blender simulation/repeat/for-each geometry zone docs, OpenMM/OpenMMTools/OpenFE protocol docs, MDAnalysis align/contacts/trajectory-transform references, MDTraj RMSD/compute_contacts API docs, Gemmi CIF/model docs, MMseqs2/Foldseek docs, and Biopython SeqIO/AlignIO/pairwise APIs align containerized compute with reproducible molecular-data ingest and visualization workflows.

Reference ledger

Read and watch the sources directly.

Back to Evidence Methods

protocolAccessed May 16, 2026 (current 1.19.0 docs)

Installing the NVIDIA Container Toolkit — NVIDIA Container Toolkit

NVIDIA

Containerized GPU runtime and viewer-state lane

Read and watch the sources directly.

Installing the NVIDIA Container Toolkit — NVIDIA Container Toolkit

Specialized Configurations with Docker — NVIDIA Container Toolkit

docker container run | Docker Docs

BuildKit | Docker Docs

Cache storage backends | Docker Docs

docker buildx bake | Docker Docs

Dockerfile reference | Docker Docs

docker buildx build | Docker Docs

docker buildx imagetools create | Docker Docs

Checking your build configuration | Docker Docs

Build checks | Docker Docs

Validating build inputs with policies | Docker Docs

docker scout cves | Docker Docs

docker scout compare | Docker Docs

docker scout sbom | Docker Docs

View and create SBOMs | Docker Docs

Get started with Policy Evaluation in Docker Scout | Docker Docs

docker scout policy | Docker Docs

docker scout quickview | Docker Docs

docker scout recommendations | Docker Docs

View Docker Scout policy status | Docker Docs

Remediation with Docker Scout | Docker Docs

Build secrets | Docker Docs

Build cache invalidation | Docker Docs

Multi-stage builds | Docker Docs

Provenance attestations | Docker Docs

Build attestations | Docker Docs

SBOM attestations | Docker Docs

Attestations | Docker Docs

Compose Build Specification | Docker Docs

Annotations | Docker Docs

GitHub Actions cache | Docker Docs

Cache management with GitHub Actions | Docker Docs

Run Docker Compose services with GPU access | Docker Docs

Containers — Nextflow documentation

Distribution and Reproducibility | Snakemake 9.21.0 documentation

Support for Docker and OCI Containers — Apptainer User Guide 1.4 documentation

apptainer oci — Apptainer User Guide main documentation

Fakeroot feature — Apptainer User Guide main documentation

Build a Container — Apptainer User Guide 1.4 documentation

apptainer build — Apptainer User Guide main documentation

apptainer config fakeroot — Apptainer User Guide main documentation

OCI Runtime Support — Apptainer User Guide main documentation

OCI Image Registries — Apptainer User Guide main documentation

GPU and other Device Support — Apptainer User Guide main documentation

GPU Support (NVIDIA CUDA & AMD ROCm) — SingularityCE User Guide latest documentation

Bind Paths and Mounts — Apptainer User Guide 1.3 documentation

Limiting Container Resources — Apptainer User Guide main documentation

Persistent Overlays — Apptainer User Guide main documentation

Installing Apptainer — Apptainer Admin Guide main documentation

Data Containers — SingularityCE User Guide 4.4 documentation

Welcome to BioContainers’s documentation!

Quick Start — micromamba-docker 2.6.1 documentation

datasets CLI tool reference

Creating Instance - Mol* Developer Documentation

Managing the display - Mol* Viewer Documentation

Making Selections - Mol* Viewer Documentation

Integrations - Mol* Viewer Documentation

Query Parameters - Mol* Viewer Documentation

Quick Styles - Mol* Viewer Documentation

URL Parameters - Mol* Viewer Documentation

Viewport Settings - Mol* Mesoscale Explorer Documentation

Measurements - Mol* Viewer Documentation

MolViewSpec Documentation

Usd : Universal Scene Description (Core) — Universal Scene Description 26.05 documentation

Python API & Text Editor - Blender Developer Documentation

Python API - Blender Developer Documentation

Python API - Blender Developer Documentation

Python API - Blender Developer Documentation

Python API - Blender Developer Documentation

Python API - Blender Developer Documentation

How to Create Extensions - Blender 5.1 Manual

The OpenMM Cookbook & Tutorials — OpenMM Cookbook & Tutorials dev documentation

Getting Started with OpenMM — OpenMM Cookbook & Tutorials dev documentation

Alchemical Free Energy Calculations — OpenMM Cookbook & Tutorials dev documentation

OpenMMTools — openmmtools documentation

Getting started tutorial — openmmtools documentation

Welcome to OpenFE’s documentation! — OpenFE documentation