The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Open accessAbstract
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.
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IQ-TREE is an integral component of many popular open-source applications such as Galaxy, Nextstrain, OrthoFinder, and QIIME 2.
“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).”
From IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2020) · cites this paper as Afgan et al. 2018
IQ-TREE is a widely used and open-source software package for phylogenetic inference using maximum likelihood.
“IQ-TREE is a widely used and open-source software package for phylogenetic inference using the maximum likelihood (ML) criterion.”
From IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2020) · cites this paper as Afgan et al. 2018
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Self-citation
- Authors
- Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A., & Blankenberg, D.
- Affiliations
- Johns Hopkins University (US)
- University of Freiburg (DE)
- Institut Curie, PSL Research University, Paris, France
- Pennsylvania State University (US)
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
- Erasmus MC (NL)
- Oregon Health & Science University (US)
- Earlham Institute (GB)
- Cleveland Clinic (US)
- Corresponding author
- Blankenberg, Daniel
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-22
- Volume
- 46
- Issue
- W1
- Pages
- W537-W544
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6030816
- OpenAlex
- W2917207851
- Cited by
- 3,662
- References
- 42
- Citations by year
- 2026: 203 · 2025: 303 · 2024: 412 · 2023: 522 · 2022: 654 · 2021: 645 · 2020: 543 · 2019: 327 · 2018: 49 · 2015: 1 · 2014: 1
- FWCI
- 559.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- HAL (submittedVersion, other-oa)
- FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- Funders
- National Institutes of Health (HG006620, HG005133, HG004909, HG005542)
- NSF (DBI 0543285, 0850103, 1661497)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Galaxy platform, web-based analysis tool, reproducible analysis, open source software, genomic data analysis, biomedical data analysis, user interface, software framework, community development, training materials
- MeSH terms
- Humans, International Cooperation, User-Computer Interface, Reproducibility of Results, Internet, Genomics, Information Dissemination, Proteomics, Metabolomics, Molecular Imaging, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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