The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Top Cited Papers
Open Access
- 22 May 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 46 (W1), W537-W544
- https://doi.org/10.1093/nar/gky379
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.Funding Information
- National Institutes of Health (HG006620, HG005133, HG004909, HG005542)
- NSF (DBI 0543285, 0850103, 1661497)
This publication has 41 references indexed in Scilit:
- GEMINI: Integrative Exploration of Genetic Variation and Genome AnnotationsPLoS Computational Biology, 2013
- Web-based visual analysis for high-throughput genomicsBMC Genomics, 2013
- The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloudNucleic Acids Research, 2013
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- BioStar: An Online Question & Answer Resource for the Bioinformatics CommunityPLoS Computational Biology, 2011
- QIIME allows analysis of high-throughput community sequencing dataNature Methods, 2010
- BLAST+: architecture and applicationsBMC Bioinformatics, 2009
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial CommunitiesApplied and Environmental Microbiology, 2009
- A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendlyGenome Research, 2007
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003