Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.
Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.
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DOI：
10.1099/mgen.0.000093
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发表时间：
2016-11
影响因子：
3.9
通讯作者：
Aanensen DM
中科院分区：
文献类型：
--
作者：
Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
可视化经常用于帮助我们解释复杂的数据集。在微生物基因组学中，将多个基因组之间的关系可视化为树提供了一个框架，在此框架上添加相关数据（地理、时间、表型和流行病学），以产生假设并探索所调查系统的动态。然后在出版物中使用选定的静态图像，向更广泛的受众突出主要发现。然而，这些图像对于探索和解释数据的丰富性来说是非常不足的。因此，需要一种灵活的交互式软件，以用户友好的方式为广泛的最终用户，从训练有素的生物信息学家到一线流行病学家和卫生工作者，提供人口基因组产出和相关数据。在这里，我们介绍Microreact，这是一个web应用程序，可以方便地可视化数据集，包括任何树、地理、时间和相关元数据的组合。数据文件可以通过web浏览器直接上传到Microreact，或者通过链接到它们的位置（例如从谷歌Drive/Dropbox或通过API），通过树、地图、时间表和表格的集成可视化提供了数据的交互式查询。可视化可以作为合作者之间的永久网络链接共享，或者嵌入到出版物中，使读者能够探索和下载数据。Microreact可以作为任何工具或生物信息学管道的终点，最终生成树，并提供简单而强大的可视化方法，有助于研究和发现以及数据集的开放共享。
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.