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. 2021 Apr 2;20(4):2056-2061.
doi: 10.1021/acs.jproteome.0c00904. Epub 2021 Feb 24.

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Jingwen Bai  1 , Chakradhar Bandla  1 , Jiaxin Guo  2 , Roberto Vera Alvarez  3 , Mingze Bai  4 , Juan Antonio Vizcaíno  1 , Pablo Moreno  1 , Björn Grüning  5 , Olivier Sallou  6 , Yasset Perez-Riverol  1
Affiliations

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Jingwen Bai et al. J Proteome Res. .

Abstract

BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize software containers including the metadata, versions, licenses, and software dependencies. BioContainers supports multiple packaging and container technologies such as Conda, Docker, and Singularity. The BioContainers provide over 9000 bioinformatics tools, including more than 200 proteomics and mass spectrometry tools. Here we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). The BioContainers Registry provides a fast and convenient way to find and retrieve bioinformatics tool packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.

Keywords: BioContainers; cloud; computational proteomics; high-performance computing; large-scale data analysis.

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Figures

Figure 1
Figure 1
Docker, Conda, and Singularity tags available for the peptide-shaker tool. The tag is a unique identifier for each registry to find and retrieve a package or container. The full tag is the combination of the repository or registry, the tool name, and the container/package tag.
Figure 2
Figure 2
The BioContainers Registry page for the peptide-shaker tool. The readme panel contains information about the tool including a general description, license, tool home page, versions, and external identifiers (e.g., PubMed). The full-page is a general description of how to install and update the specific tool for each of the provided technologies: Conda, Docker, or Singularity.
Figure 3
Figure 3
a) Distribution of per-container downloads (log scale), separated by specific omics category: Transcriptomics, Proteomics, Metabolomics and Genomics. Black dots in the extreme of every plot represent outliers, dark bars represent the interval between upper and lower quartiles. b) List of most downloaded proteomics tools from BioContainers, the term others group more than 200 proteomics tools in the registry not included in the plot.
See this image and copyright information in PMC

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