The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

By E. Afgan, D. Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, J. Chilton, D. Clements, Nate Coraor, Björn A. Grüning and 10 more. Nucleic Acids Res., 2018

1,614 citations recorded by the source corpus.

Abstract Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f58e82a426c90f8c86efa442bef87dfc6fcf04f6

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Citations in the corpus

Structural model of PORCN illuminates disease-associated variants and drug binding sites (2021, positive): “Lastly, the simulated structure was refined by GalaxyRefine2 from GalaxyWEB (Afgan et al., 2018; Boekel et al., 2015) to generate the final predicted structure.”
Sustainable data analysis with Snakemake (2021, neutral): “First, workﬂow management systems like Galaxy [1], often referred to as “science gateways“ [2], oﬀer graphical, web-based user interfaces for composition and execution of workﬂows.”
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) (2019, methodology): “For example, g:Profiler serves its users via a web client and API, Python and R packages, and is available as a tool for Galaxy platform (10).”
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2019, background): “For instance, it is an integral component of many popular open-source applications such as Galaxy (Afgan et al. 2018), Nextstrain (Hadfield et al. 2018), OrthoFinder (Emms and Kelly 2015), and QIIME 2 (Bolyen et al. 2019).”
NGPhylogeny.fr: new generation phylogenetic services for non-specialists (2019, background): “In parallel, scientific workflow systems (Galaxy (11,12)) have reached a level of maturity that makes them convenient for scheduling the execution of complex and large-scale analyses, while properly managing data by tracking consumed and produced data.”