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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
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 h...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320705/ https://www.ncbi.nlm.nih.gov/pubmed/28348833 http://dx.doi.org/10.1099/mgen.0.000093 |
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author | Argimón, Silvia Abudahab, Khalil Goater, Richard J. E. Fedosejev, Artemij Bhai, Jyothish Glasner, Corinna Feil, Edward J. Holden, Matthew T. G. Yeats, Corin A. Grundmann, Hajo Spratt, Brian G. Aanensen, David M. |
author_facet | Argimón, Silvia Abudahab, Khalil Goater, Richard J. E. Fedosejev, Artemij Bhai, Jyothish Glasner, Corinna Feil, Edward J. Holden, Matthew T. G. Yeats, Corin A. Grundmann, Hajo Spratt, Brian G. Aanensen, David M. |
author_sort | Argimón, Silvia |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5320705 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-53207052017-03-27 Microreact: visualizing and sharing data for genomic epidemiology and phylogeography Argimón, Silvia Abudahab, Khalil Goater, Richard J. E. Fedosejev, Artemij Bhai, Jyothish Glasner, Corinna Feil, Edward J. Holden, Matthew T. G. Yeats, Corin A. Grundmann, Hajo Spratt, Brian G. Aanensen, David M. Microb Genom Research Paper 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. Microbiology Society 2016-11-30 /pmc/articles/PMC5320705/ /pubmed/28348833 http://dx.doi.org/10.1099/mgen.0.000093 Text en © 2016 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Paper Argimón, Silvia Abudahab, Khalil Goater, Richard J. E. Fedosejev, Artemij Bhai, Jyothish Glasner, Corinna Feil, Edward J. Holden, Matthew T. G. Yeats, Corin A. Grundmann, Hajo Spratt, Brian G. Aanensen, David M. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title_full | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title_fullStr | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title_full_unstemmed | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title_short | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
title_sort | microreact: visualizing and sharing data for genomic epidemiology and phylogeography |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320705/ https://www.ncbi.nlm.nih.gov/pubmed/28348833 http://dx.doi.org/10.1099/mgen.0.000093 |
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