Revision 45028bfdd7827cb1b14c5993c7c7b6971d44597b authored by Kathy Tran on 03 March 2023, 14:38:52 UTC, committed by Kathy Tran on 03 March 2023, 14:38:52 UTC
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citation.cff
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."
authors:
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Yuen
given-names: Denis
orcid: "https://orcid.org/0000-0002-6130-1021"
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Cabansay
given-names: Louise
orcid: "https://orcid.org/0000-0002-1475-5979"
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Duncan
given-names: Andrew
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Luu
given-names: Gary
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Hogue
given-names: Gregory
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Overbeck
given-names: Charles
-
family-names: Perez
given-names: Natalie
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Shands
given-names: Walt
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Steinberg
given-names: David
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Reid
given-names: Chaz
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Olunwa
given-names: Nneka
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Hansen
given-names: Richard
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Sheets
given-names: Elizabeth
orcid: "https://orcid.org/0000-0002-6335-4952"
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: "O'Farrell"
given-names: Ash
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Cullion
given-names: Kim
-
affiliation: "Data Sciences Platform, Broad Institute"
family-names: "O'Connor"
given-names: Brian
name-particle: D
-
affiliation: "UC Santa Cruz Genomics Institute"
family-names: Paten
given-names: Benedict
-
affiliation: "Ontario Institute for Cancer Research"
family-names: Stein
given-names: Lincoln
cff-version: "1.1.0"
date-released: 2021-05-12
doi: "10.1093/nar/gkab346"
license: "Apache 2.0"
message: "If you use this software, please cite it in general using this paper, particularly for Dockstore 1.10 and above"
repository-code: "https://github.com/dockstore/dockstore"
title: "The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols "
version: "1.11"
references:
- type: article
scope: "Cite this paper to reference Dockstore up to version 1.9"
title: "The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows"
year: 2017-01-18
journal: F1000Research
volume: "6"
issue: "52"
doi: "10.12688/f1000research.10137.1"
- type: software-code
scope: "Cite Zenodo when citing the source code"
title: "dockstore/dockstore"
doi: "10.5281/zenodo.592056"
version: "1.11"
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