Hackout3: analysis and modelling tools for emergency outbreak response

The recent Ebola virus disease outbreak in West Africa has been a terrible reminder of the necessities of rapid evaluation and response to emerging infectious disease threats. For such response to be fully informed, complex epidemiological data including dates of symptom onsets, locations of the cases, hospitalisation, and contact tracing information have to be analysed in near real time. Unfortunately, some of the tools required to bridge the gap between data collection in regional offices and advanced statistical modelling are still lacking.

Hackout 3 will aim to reduce this gap by bringing together field epidemiologists, decision makers, modellers and computer scientists to create free, open-source resources for the real-time monitoring of disease outbreaks. While new developments will largely build upon recent progresses for epidemics analysis using the R software, other technologies will also be considered, including existing tools for data collection (e.g. EpiInfo VHF), graph databases (Neo4j) and interactive, web-based graphs (e.g. htmlwidgets, shiny, google charts).

The Participants

We are assembling an exciting team of people interested in developing the next generation of tools for outbreak response, including modellers, statisticians, developers and public health workers.

Note: this list will be growing over the next few days as participants are being confirmed. The event should involve 30-40 people in total.

Finlay Campbell

Imperial College London

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Elisabeth Dahlqwist

Karolinska Institutet

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Rich FitzJohn


Imperial College London, rOpenSci (UK)

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Shikun Li


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Vijay Peter Nagraj

University of Virginia

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Katie Planey


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Jonathan Polonsky

World Health Organisation

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Armand Sprecher

Médecins Sans Frontières


Maria Van-Kerkhove


Institut Pasteur

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Edwin Van Leuuwen

Public Health England

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Oliver Watson

Imperial College London

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Nicole White


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Dani Ushizima

Lawrence Berkeley National Laboratory

Join us!

• We want to: create the next generation of free, open-source tools for disease outbreak response.

• We are looking for: infectious disease modellers, statisticians, public health workers, programmers, web developers, database experts...

• We aim to: maximize diversity in skills, experiences, and people.

• Applications closed on the 15th April 2016.

The Venue

Hackout 3 will be hosted at the Berkeley Institute for Data Science. Follow the official directions, or see the map below:


Funded participants will be hosted at the DoubleTree Hilton Hotel in the Marina, Berkeley. The hotel is about 10-15 min by taxi to the venue.

Schedule of events

Hackout 3 will be a five-days event, including a first day of brainstorming, leaving most of the rest of the time for developing tools, discussing methods, and testing new approaches. The Wednesday afternoon will be free, with possibility of a group hike for participants interested in seeing a bit of the nature surrounding Berkeley.

Every day will start with breakfast at 9-10am and finish at 6pm. Lunch will be served around 12:30.

The Sponsors

We are extremely grateful to our sponsors for this third instance of Hackout.

Hackout 3 is co-supported by:

If you would like to sponsor Hackout 3, please contact us via email.

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