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

Jingwen Bai · Chakradhar Bandla · Jiaxin Guo · Roberto Vera Alvarez · Mingze Bai · Juan Antonio Vizcaíno +4 more

31 citations0/0 files storedJournal of Proteome Research

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Scientific Computing and Data Management Genomics and Phylogenetic Studies Research Data Management Practices

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.

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2017Nextflow enables reproducible computational workflows 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update 2012Snakemake—a scalable bioinformatics workflow engine 2017Singularity: Scientific containers for mobility of compute 2018Bioconda: sustainable and comprehensive software distribution for the life sciences 2017BioContainers: an open-source and community-driven framework for software standardization 2018Snakemake—a scalable bioinformatics workflow engine 2017Four simple recommendations to encourage best practices in research software

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