Reticulate workflows for complex decision making – an example from an emergency animal disease decision support system

Kerryne Graham1, Duan Beckett2, Justin Freeman2, Chris Cowled3, Marcus Thatcher4, Peter Hurley5, Michael Newton6, William Scobell6, Peter Durr1

1CSIRO Australian Animal Health Laboratory, Geelong, Australia, 2Bureau of Meteorology, Melbourne, Australia, 3CSIRO Health & Biosecurity, Geelong, Australia, 4CSIRO Oceans and Atmosphere, Aspendale, Australia, 5CSIRO Oceans and Atmosphere , Black Mountain, Australia, 6NewtonGreen Technologies Pty Ltd, Newcastle, Australia

Abstract:

Introduction: The workflow concept is fundamental to decision support systems (DSS). This applies particularly to DSS used in national emergencies, such as bush-fires, floods, public health and animal health epidemics. Traditionally, emergency management DSS have used a “linear” workflow, whereby users are assumed to have a defined starting point (with respect to knowledge and data) and a clear end point which leads to an optimum decision.

Methods: We are developing a high-level framework of multi-stage workflows where end-user access is via a web interface and requests for data analyses and modelling are undertaken via an application programming interface (API) and completed on a high-performance computing infrastructure.

Results:  Given the objective of providing a DSS for emergency animal diseases (EAD), we have developed SPREAD, a system of determining how an epidemic disease is spreading either within a farm or between farms. SPREAD provides visualisation of the epidemic in space and time, assessing of the role of wind dispersion, next generation sequence (NGS) assembly and annotation, and finally construction of various transmission networks.

Conclusion:  The concept of integrating whole-genomic sequencing data with wind dispersion modelling was developed from the experience of the 2007 UK Foot-and-Mouth Disease outbreak. However, this pioneering work was undertaken retrospectively, and to date no system has been developed that will enable transmission pathways to be determined in near real-time.  SPREAD enables animal health managers and veterinary officers to efficiently use meteorology and NGS data in reticulated workflows for effective EAD management.


Biography:

Kerryne works within the Veterinary Investigation and Epidemiology team located at the Australian Animal Health Laboratory. She is involved in several collaborative projects where she is able to apply her expertise in data management, spatial analysis and implementation of surveillance information systems.    Kerryne has most recently been involved in modelling the habitat suitability for the effective release of Cyprinid Herpes virus-3 for the control of European Carp and is also a team member of  SPREAD – a web application integrating epidemic data, wind-dispersion and molecular data for surveillance and response.

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