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dc.contributor.authorArgimón, Silvia
dc.contributor.authorAbudahab, Khalil
dc.contributor.authorGoater, Richard J. E.
dc.contributor.authorFedosejev, Artemij
dc.contributor.authorBhai, Jyothish
dc.contributor.authorGlasner, Corinna
dc.contributor.authorFeil, Edward J.
dc.contributor.authorHolden, Matthew T. G.
dc.contributor.authorYeats, Corin A.
dc.contributor.authorGrundmann, Hajo
dc.contributor.authorSpratt, Brian G.
dc.contributor.authorAanensen, David M.
dc.date.accessioned2016-12-02T13:30:11Z
dc.date.available2016-12-02T13:30:11Z
dc.date.issued2016-11-30
dc.identifier.citationArgimón , S , Abudahab , K , Goater , R J E , Fedosejev , A , Bhai , J , Glasner , C , Feil , E J , Holden , M T G , Yeats , C A , Grundmann , H , Spratt , B G & Aanensen , D M 2016 , ' Microreact: visualizing and sharing data for genomic epidemiology and phylogeography ' , Microbial Genomics , vol. 2 , no. 11 . https://doi.org/10.1099/mgen.0.000093en
dc.identifier.issn2057-5858
dc.identifier.otherPURE: 248115969
dc.identifier.otherPURE UUID: a642021a-eaa9-4b4b-9dcb-46e2a5d13b5b
dc.identifier.otherBibtex: urn:26f744d696057f175b358170ff0de31d
dc.identifier.otherScopus: 85011113621
dc.identifier.otherORCID: /0000-0002-4958-2166/work/60196494
dc.identifier.otherWOS: 000431154300002
dc.identifier.urihttp://hdl.handle.net/10023/9925
dc.description.abstractVisualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
dc.format.extent11
dc.language.isoeng
dc.relation.ispartofMicrobial Genomicsen
dc.rights© 2016 The Authors. Published by Microbiology Society. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).en
dc.subjectOpen dataen
dc.subjectTreesen
dc.subjectPhylogenomicsen
dc.subjectPopulation genomicsen
dc.subjectPhylogeographyen
dc.subjectQH426 Geneticsen
dc.subjectGE Environmental Sciencesen
dc.subjectZ665 Library Science. Information Scienceen
dc.subjectZA4050 Electronic information resourcesen
dc.subjectDASen
dc.subject.lccQH426en
dc.subject.lccGEen
dc.subject.lccZ665en
dc.subject.lccZA4050en
dc.titleMicroreact: visualizing and sharing data for genomic epidemiology and phylogeographyen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.contributor.institutionUniversity of St Andrews.Infection Groupen
dc.contributor.institutionUniversity of St Andrews.Biomedical Sciences Research Complexen
dc.identifier.doihttps://doi.org/10.1099/mgen.0.000093
dc.description.statusPeer revieweden


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