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Digital Methods in Epidemiology

March 30

Last week, we had the pleasure of attending a day-long meeting on ‘Digital Methods in Epidemiology’ hosted by the Royal Society of Tropical Medicine and Hygiene (@RSTMH) hosted at SOAS, University of London.

The event drew speakers from academia and industry (Microsoft) that are integrating various digital technologies into health-related research. On show were a variety of methodologies, from web-based applications for gathering epidemiological data, drones for monitoring land use changes, platforms for collating internet reports of infectious diseases (including user-based verification), genetics applications to monitor evolutionary change in various infectious bugs, and much more.

Prof Dominic Kwiatkowski speaking about MalariaGEN’s work studying natural genetic variation in both P. falciparum and Anopheles mosquitoes.As part of a great line-up of speakers, CGGH Director Prof Dominic Kwiatkowski spoke about MalariaGEN’s work studying natural genetic variation in both P. falciparum and Anopheles mosquitoes, and gave a demo of the Panoptes-based applications that serve data from the Pf3k and Ag1000G consortia.

The meeting was organized to launch a special issue of International Health focused on the same topic, which will be available open access until 30 April 2015.

Select resources & tools

Below are links to some of the publicly available resources that were presented on the day.

MLST - http://www.mlst.net/
MLST (Multi Locus Sequence Typing) is a nucleotide sequence-based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The tool can be used to evaluate individual allele frequencies, allelic profiles, sequence types – and can be used to build dendograms to identify allelic mismatches, clones and closely related strains.

eBURSTv3 - http://eburst.mlst.net/
eBURST allows researchers to go from single variants to clonal complexes and can predict the founding sequence type in each group. This tool can be used to overlay information on presence or absence of drug resistance, and has been used to define major epidemic clones.

Microreact - http://microreact.org/
Microreact makes data accessible to labs that have participated in a variety of studies, using standardised methods to identify the origins and spread of resistance in near real-time.

EpiCollect - http://www.epicollect.net/
Epicollect is a tool for creating forms for data collection on mobile. The results can be collated and viewed in a web application. About 14,000 projects of every size and shape are set up on EpiCollect including, for example, a project that is vaccinating dogs in India against rabies and an FAO project that is tracking information about Ebola infection in Liberia.

Panoptes - https://github.com/cggh/panoptes
The Panoptes software framework can be rapidly deployed to create interactive web applications for exploring genetic and genomic data, while also supporting a high level of customisation to suit the unique nature of particular datasets and projects. Two early implementations of this framework are web applications are designed to share data from the Anopheles gambiae 1000 Genomes Project (Ag1000G) and Pf3k projects.

Ag1000G web application - http://www.malariagen.net/apps/ag1000g
The current version contains data on 765 mosquito specimens collected from eight countries and sequenced by the Wellcome Trust Sanger Institute Malaria Programme. For more information on these data, see the Ag1000G phase 1 AR2 data release web page.

Take a video tour of the Ag1000G web application: https://www.youtube.com/watch?v=LWCbi8t9Zug

Pf3k web application - http://www.malariagen.net/apps/pf3k
The current version contains sample information, accession numbers and genotypes for 1,931 samples comprised of the 1,794 samples included in the Pf3k 1.0 pilot release along with an additional 137 samples contributed by the Broad Institute. For more information about these data, visit the Pf3k pilot data release 2 web page.

World Pop - http://www.worldpop.org.uk/
Follow along @WorldPopProject
High resolution, contemporary data on human population distributions are a prerequisite for the accurate measurement of the impacts of population growth, for monitoring changes and for planning interventions. The WorldPop project aims to meet these needs through the provision of detailed and open access population distribution datasets built using transparent approaches.

Flowminder - http://www.flowminder.org/
Flowminder is using anonymised mobile phone network data, household surveys, and remote sensing data to improve planning and operational decision making in a range of areas including disease outbreak prevention.

ABRAID - https://www.abraid.ox.ac.uk/
Follow along @ABRAID_group
The Atlas of Baseline Risk Assessment for Infectious Diseases (ABRAID) recently launched a beta website that aims to produce continually updated maps of disease risk with contributions from experts.

Healthmap - www.healthmap.org
Follow along @healthmap
A global disease alert surveillance system that utilizes online informal sources for information about disease outbreaks to provide real-time surveillance of emerging public health threats. The platform was founded in 2006, and developed by a team of researchers, epidemiologists and software developers at Boston Children's Hospital in the USA.

Watch their video to learn more: https://vimeo.com/27433633