{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T13:12:56Z","timestamp":1760015576010,"version":"3.38.0"},"reference-count":19,"publisher":"China Science Publishing & Media Ltd.","issue":"2","license":[{"start":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T00:00:00Z","timestamp":1651017600000},"content-version":"vor","delay-in-days":116,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2022,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Despite recent encouragement to follow the FAIR principles, the day-to-day research practices have not changed substantially. Due to new developments and the increasing pressure to apply best practices, initiatives to improve the efficiency and reproducibility of scientific workflows are becoming more prevalent. In this article, we discuss the importance of well-annotated tools and the specific requirements to ensure reproducible research with FAIR outputs. We detail how Galaxy, an open-source workflow management system with a web-based interface, has implemented the concepts that are put forward by the Canonical Workflow Framework for Research (CWFR), whilst minimising changes to the practices of scientific communities. Although we showcase concrete applications from two different domains, this approach is generalisable to any domain and particularly useful in interdisciplinary research and science-based applications.<\/jats:p>","DOI":"10.1162\/dint_a_00136","type":"journal-article","created":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T14:39:01Z","timestamp":1651070341000},"page":"358-371","update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":9,"title":["Galaxy: A Decade of Realising CWFR Concepts"],"prefix":"10.3724","volume":"4","author":[{"given":"Beatriz","family":"Serrano-Solano","sequence":"first","affiliation":[{"name":"Bioinformatics Group, University of Freiburg, Baden-W\u00fcrttemberg 79098, Germany"}]},{"given":"Anne","family":"Fouilloux","sequence":"additional","affiliation":[{"name":"Department of Geosciences, University of Oslo, Oslo 0316, Norway"}]},{"given":"Ignacio","family":"Eguinoa","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium"},{"name":"VIB, Gent, Oost-Vlaanderen 9052, Belgium"}]},{"given":"Mat\u00fa\u0161","family":"Kala\u0161","sequence":"additional","affiliation":[{"name":"Department of Informatics, University of Bergen Ringgold standard institution, University of Bergen, Bergen, Hordaland 5008, Norway"}]},{"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, University of Freiburg, Baden-W\u00fcrttemberg 79098, Germany"}]},{"given":"Frederik","family":"Coppens","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium"},{"name":"VIB, Gent, Oost-Vlaanderen 9052, Belgium"}]}],"member":"2026","published-online":{"date-parts":[[2022,4,1]]},"reference":[{"key":"2022042714321590600_ref1","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.future.2017.05.041","article-title":"Scientific workflows: Past, present and future","volume":"75","author":"Atkinson","year":"2017","journal-title":"Future Generation Computer Systems"},{"issue":"1","key":"2022042714321590600_ref2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1162\/dint_a_00084","article-title":"Not ready for convergence in data infrastructures","volume":"3","author":"Jeffery","year":"2021","journal-title":"Data Intelligence"},{"key":"2022042714321590600_ref3","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biology"},{"issue":"W1","key":"2022042714321590600_ref4","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Research"},{"volume-title":"Canonical Workflow Framework for Research (CWFR)\u2014position paper\u2014 version 2, December 2020","author":"Hardisty","key":"2022042714321590600_ref5"},{"volume-title":"EDAM: The bioscientific data analysis ontology (update 2021) [version 1; 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