Singularity: Scientific containers for mobility of compute

By G. M. Kurtzer, Vanessa V. Sochat, Michael Bauer. PLoS ONE, 2017

2,468 citations recorded by the source corpus.

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.

Subfields: Computer Networks and Communications, Information Systems, Information Systems and Management

View Paper: https://www.semanticscholar.org/paper/8399752a2e594098e8d5cc813d6a7fc95af2e07f

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Citations in the corpus

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data (2019, methodology): “Access to the necessary bioinformatic tools is also facilitated through the use of Singularity containers (43), which eliminates the need for ‘sudo’ access in computing clusters.”
Unreproducible Research is Reproducible (2019, background): “More tools are made available to simplify the replication of experiments reported in papers, building on new technologies such as shareable notebooks (Kluyver et al., 2016; Forde et al., 2018), containerization of operation systems, such as Docker (Merkel, 2014) and Singularity (Kurtzer et al., 2017”
A scalable SCENIC workflow for single-cell gene regulatory network analysis (2020, methodology): “In this case, no compiling or installation is required, provided either Docker (https://www.docker.com/) or Singularity 21 software is installed on the user ’ s system.”
Auto-Sklearn 2.0: Hands-free AutoML via Meta-Learning (2020, methodology): “Therefore, we extended the AutoML benchmark with support for Singularity images (Kurtzer et al., 2017), and used them to isolate the framework installations from each other.”
Automated assessment of psychiatric disorders using speech: A systematic review (2019, methodology): “rerun easily to re-execute original analyses or replicate analyses on other data.(139,140) Innovation might be faster if models could be tweaked in a more efficient manner.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update (2020, methodology): “This coherence is realized by a multitude of components including a public repository of all 7500+ tools integrated into Galaxy, named ToolShed (1), a public repository of over 36,000 Singularity containers (17) for all Bioconda packages (18) that provide the software dependencies for Galaxy tools, ”
The IllustrisTNG simulations: public data release (2018, methodology): “These are spawned inside containerized Docker instances (Merkel 2014) to isolate the user from the host systems—Singularity (Kurtzer et al. 2017) could be used in the future.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, background): “com) and Singularity (35)) to ensure a higher level of portability, if needed.”
The NANOGrav 15 yr Data Set: Observations and Timing of 68 Millisecond Pulsars (2023, methodology): “A Singularity (Kurtzer et al. 2017) container, which is optimized for HPC workloads.”
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, positive): “Additionally, BRAKER3 adds a Docker container that also easily executes with Singularity (Kurtzer et al., 2017) to the BRAKER suite, which makes it more user-friendly and easier to install.”