The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Abstract Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interope...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 49; no. W1; pp. W624 - W632
Main Authors:	Yuen, Denis, Cabansay, Louise, Duncan, Andrew, Luu, Gary, Hogue, Gregory, Overbeck, Charles, Perez, Natalie, Shands, Walt, Steinberg, David, Reid, Chaz, Olunwa, Nneka, Hansen, Richard, Sheets, Elizabeth, O’Farrell, Ash, Cullion, Kim, O’Connor, Brian D, Paten, Benedict, Stein, Lincoln
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 02-07-2021
Subjects:	Cloud Computing Computational Biology - education Computational Biology - methods Data Visualization Humans Information Dissemination Internet National Heart, Lung, and Blood Institute (U.S.) National Human Genome Research Institute (U.S.) Reproducibility of Results Software United States Web Server Issue Workflow United States
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Summary:	Abstract Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute's GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content. Graphical Abstract Graphical Abstract Dockstore: enhancing an open platform for sharing Docker-based tools described with workflow languages for the sciences.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
ISSN:	0305-1048 1362-4962
DOI:	10.1093/nar/gkab346