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Digital tools for data collection and analysis: EMPRES and Imperial College London to collaborate on advanced field data analysis

01 February 2017 - Recent developments in technology combined with worldwide availability and usage of mobile devices provide epidemiologists and virologists around the globe with new possibilities for collection, analysis, visualization, storage and sharing of data. On 11 and 12 January 2017, representatives from Imperial College London met with FAO staff in Rome to discuss future collaboration and pave the way forward for the use of new digital tools in FAO projects.

In the framework of the Emerging Pandemic Threats Phase 2 (EPT-2) Program, funded by the United States Agency for International Development (USAID), FAO plans to carry out a suite of activities targeted at the animal-human-ecosystem interface, fostering interdisciplinary collaboration to integrate knowledge on agro-ecological, anthropogenic, socio-economic and demographic disease drivers. To collect and analyze this substantial amount of field data, an assessment of available applications for field data collection was conducted in mid-2016. After careful evaluation of existing solutions and their field testing in Kenya, Tanzania and Senegal, the application Epicollect5 developed by Dr Aanensen and his team at Imperial College London struck as the optimal choice for FAO’s activities under the EPT-2 project.

As sampling activities are due to start in Africa, national teams from FAO, veterinary services and laboratories are being equipped with Android tablet devices and trained on the use of the mobile application. The team at Imperial College has been providing technical assistance for troubleshooting and are collaborating to introduce additional features to better fit the project’s needs.

To firm up this collaboration, Dr David Aanensen and developers Mirko Menegazzo and Antonio Puleo met with the EMPRES team at the FAO headquarters in Rome, Italy. Feedback from preliminary field testers and latest developments were reviewed before discussions were held on technical aspects related to optimizing the tools and their usage for wider rollout within the EPT-2 project.

EMPRES used this visit as an opportunity to present these tools to other FAO departments. A seminar entitled ‘Use of digital tools for epidemiological and virological data collection and analysis’ was held on the second day of the meeting. The seminar recording is accessible online HERE. The Imperial College team presented three of their applications: Epicollect51, Microreact2 and WGSA3. Since these applications have been developed as generic tools they are applicable to a wide range of purposes, as showcased by many existing examples. A live demonstration further illustrated user-friendliness and functionality. 


1 Epicollect5 is an android/iOS mobile application designed for field data collection. It allows any user to create a questionnaire from a web application, to upload it onto multiple mobile devices (phone or tablet), from which data can be collected and then synchronized with a cloud server. http://five.epicollect.net

2 Microreact is a tool for open data sharing for genomic epidemiology and phylogeography and allows users to upload, visualize and share their data, consisting of combination of clustering (genetic trees), geographic (map) and temporal (timeline) data.

3 WGSA (Whole Genome Sequencing Analysis) is a system focused on genomic surveillance of pathogens enabling the processing of microbial genome assemblies and metadata to generate results such as phylogenetic trees, multilocus sequence typing and antimicrobial resistance predictions. Results are presented through interactive visualization of metadata.


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