Easily create Interactive web visualisations using Maps, phylogenetic trees and metadata.
Developed at Imperial College London with aditional development within CGPS Microreact is available at http://microreact.org
Microreact allows users to upload, visualise and explore dendrograms (trees) linked to geographic locations. Additionally, any number of metadata fields can be defined and users can specify colours and/or shapes to display on map/tree. Data without colour/shape definitions are available to display as text labels next to each tree leaf and within tables. Furthermore, if temporal data (day/month/year) are included, a time slider allows the filtering of data based on time window.
Many sequencing pipelines exist for processing raw data. In most cases, and in particular within microbial genomics, the output are used to cluster more similar genomes in the form of a tree and the clustering patterns are used with available epidemiological, phenotypic and genotypic metadata to explore the datasets (eg outbreak investigations). While there are many pipelines in the wild, the end points (tree / is traditionally done using static images). We developed MicroReact to provide simple intuitive online visualisations for quicker, simpler investigations, for sharing and to promote reproducibility. MicroReact provides a simple solution for data visualisation and interpretation.
Our mission is to inform control strategies and interventions on a local, national and international scale. Our group consists of a mix of genomic epidemiologists, computational biologists and web software engineers within The Centre for Genomic Pathogen Surveillance (CGPS) a collaboration with the Big Data Institute, University of Oxford.
We are using genomics to get at important problems in infectious disease, with a strong desire to translate this into tools for disease control and elimination, but we are also at the forefront of basic research into microbial ecology, evolutionary genetics and the biology of parasitism.