Examples
Worked examples
- Is an instance
An analysis distributed as a Docker image pinned by SHA-256 digest in a paper's reproducibility appendix.
- Is an instance
A bioinformatics image hosted on Quay.io referenced by a Nextflow pipeline.
- Is an instance
A shared HPC cluster running a bioinformatics workload from a .sif file via Singularity/Apptainer, with no root access requested or granted.
Counter-examples
Looks similar, but isn't
- Not an instance
A virtual-machine image (heavier and less portable).
- Not an instance
A conda environment YAML (specifies environment but not OS/runtime).
Editorial commentary
A container image is a packaged, immutable filesystem bundling an application together with every dependency it needs to run — system libraries, language runtime, configuration — built from a build specification (a Dockerfile for Docker, or a definition file for Singularity/Apptainer) and runnable identically across compatible host machines via a container engine.
Docker versus Singularity/Apptainer — why research computing generally uses the latter
Docker is the dominant container engine for general software deployment, but its daemon model requires root-equivalent privileges to run containers, which most shared HPC clusters will not grant to individual users. Singularity was created specifically to solve this for scientific and HPC computing: it runs containers without a privileged daemon, mapping the container process to the invoking user’s own permissions, while still consuming standard OCI/Docker-format images. In 2021 the open-source Singularity project moved to the Linux Foundation and was renamed Apptainer to resolve a naming and trademark conflict with a commercial fork, SingularityCE, maintained by Sylabs, which continued under the original name — so Singularity and Apptainer today refer to two actively maintained, closely related but organisationally separate projects descended from the same original codebase, and a citation should specify which one was actually used.
Running a Singularity container
In practice, a Singularity container is a single portable image file in Singularity Image Format (a .sif file), built once from a definition file or converted from an existing Docker/OCI image, then executed directly with no daemon and no elevated privileges required. This is the pattern documented by Sylabs’ own user guides and by university and government HPC centers alike: a shared cluster can let a researcher run a containerized workload inside a scheduled batch job without granting that user root access anywhere on the system.
Why it matters for reproducibility
A container image is one concrete mechanism for capturing a computational environment; sharing the image or its build file alongside code and data is now standard practice for computational reproducibility, and several journals now request it explicitly.
References
- Apptainer project documentation and history (apptainer.org).
- See also: Computational environment, Workflow (as output), Reproducibility Infrastructure: Workflows, Containers, and Code Sharing.
Also known as
Docker image · Singularity image · Apptainer image · OCI image · Singularity container
Machine-readable encodings
Use in your systems
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