Microreact: Visualizing and sharing data for genomic epidemiology and phylogeography
| Autor: | Artemij Fedosejev, Silvia Argimón, Khalil Abudahab, Brian G. Spratt, David M. Aanensen, Edward J. Feil, Corinna Glasner, Corin Yeats, Jyothish N Nair Thulasee Bhai, Richard Goater, Matthew T. G. Holden, Hajo Grundmann |
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| Přispěvatelé: | University of St Andrews. School of Medicine, University of St Andrews. Infection Group, University of St Andrews. Biomedical Sciences Research Complex, Wellcome Trust |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Microbiological Techniques population genomics Computer science Population QH426 Genetics Trees World Wide Web ZA4050 03 medical and health sciences 0302 clinical medicine Data file Web application education QH426 Z665 education.field_of_study Internet Molecular Epidemiology GE ZA4050 Electronic information resources business.industry End user Information Dissemination Open data Phylogenomics DAS phylogenomics General Medicine Genomics trees Hyperlink Data science Visualization Metadata Tree (data structure) Phylogeography 030104 developmental biology Microbial Evolution and Epidemiology business Population genomics 030217 neurology & neurosurgery Software GE Environmental Sciences Z665 Library Science. Information Science Research Paper |
| Zdroj: | Microbial Genomics |
| ISSN: | 2057-5858 |
| Popis: | Visualization 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. Publisher PDF |
| Databáze: | OpenAIRE |
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