DECIDE project

On July 1st 2021, a EU funded research project called DECIDE with 19 partners in 11 countries started for a period of five years. About 9 PhD students and several postdoctoral researchers are/will be hired by the partner organisations In the DECIDE project.

The DECIDE project aims at developing data-driven decision support tools, which present (i) robust and early signals of disease emergence and options for diagnostic confirmation; and (ii) options for controlling the disease along with their implications in terms of disease spread, economic burden and animal welfare.

DECIDE focusses on respiratory and gastro-intestinal syndromes in the three most important terrestrial livestock species (pigs, poultry, cattle) and on growth reduction and mortality in salmonids. For each of these, we will (i) identify the stakeholder needs; (ii) determine the burden of disease and costs of control measures; (iii) develop data sharing frameworks based on federated data access and meta-information sharing; (iv) build multivariate and multi-level models for creating an early warning system. Together, all of this will form the decision support tools to be integrated in existing farm management systems wherever possible and to be evaluated in several pilot implementations in farms across Europe.

The results of DECIDE will lead to improved decisions on disease control to increase animal health and welfare and protect human health and the food chain in Europe and beyond.

At Utrecht University and Ghent University we host four PhD students that are keen to work on the interface of data science, veterinary science and economics in an international setting. Close collaboration is foreseen with partners in the DECIDE project that identify the stakeholder needs (ETHZ, CH) and build multivariate and multi-level models for creating an early warning system (UCPH, DK). For all four positions, the candidates are team players that are able to collaborate interdisciplinary and have very good spoken and written ability in English.

Below are the descriptions of the respective PhD projects and the requirements for suitable candidates.

PhD 1. Development of data sharing frameworks based on federated data access and meta-information sharing (UGent/UU)

The main objective of this PhD project is to explore the different approaches for data access and data usage to support animal health by combining existing and new data and data streams. The Ph.D candidate will be the main responsible (in collaboration with the main supervisor).

To develop a common ontology that allows data from different sources to be interpreted consistently through-out the entire project.

To develop and test alternative approaches for data access and define best practices for sustainable data access (data-to-the-code vs code-to-the-data, federated querying, federated learning)
The preferred candidate should have a degree in a data science field, such as Applied Data Science, Genetics, and Quantitative biology. Preferably the candidate has an interest in livestock production.

Requirements:

The candidate has experience with ontology design
The candidate has an affinity with the livestock production systems
The candidate has experience with or is able to learn (statistical) programming and/or coding.
Proficiency in English, both written and oral is required.
Good communication skills are essential for this interdisciplinary and international collaboration project.
The candidate can work both on her/his own, but also enjoys interaction with an interdisciplinary team and international colleagues

The student will hold a PhD position at Ghent University in strong collaboration with Utrecht University. More information about this position can be obtained from Ass. Prof. Dr. Miel Hostens (m.m.hostens@uu.nl or miel.hostens@ugent.be ).

PhD 2. Determining the burden of disease and costs of control measures (UU) - Position taken

The main objective of this PhD project is to determine the economic and welfare burden of prevalent contagious production diseases and ensure prioritisation of control measures for reduction of further spread, cost effectiveness and in-creased welfare. More specifically, its objectives are:

To calculate the biomass of the animals and their economic value and the health loss envelope in order to understand the burden of disease.
To determine loss and expenditure frontiers of the causes and risk factors of diseases in order to assess current levels of allocation and identify additional costs and benefits of interventions.
To assess the relationship between health, diseases and welfare.
To calculate the costs and benefits of interventions.

The preferred candidate should have a degree in a quantitative field, such as animal health economics, veterinary epidemiology, genetics, and quantitative biology. Preferably the candidate has a background, but at least an interest, in livestock production. Proficiency in English, both written and oral is required. Good communication skills are essential for this interdisciplinary and international collaboration project.

More information about this position can be obtained from Dr.ir. Wilma Steeneveld.

PhD 3. Developing decision support tools to be integrated in existing farm management systems for poultry farms across Europe (UU) - Position taken

The main objective of this PhD project is to develop tools to support decisions on the management of animal health for implementation in broiler production. More specifically, the objectives are:

Surveying data sources to identify which available data is most valuable in developing monitoring models and decision support tools for infectious diseases in poultry, and help define ontologies and the methods and requirements for data access (in close collaboration with PhD1).
Determine the needs, willingness and associated expectations for the data-driven decision support tools of potential end-users and stakeholders to help them prioritise control and preventive measures to better manage respiratory and intestinal diseases.
Parameterise and use mechanistic disease model (INRAE, FR) and monitoring models (UCHP, DK) for broiler farms to provide flock specific data-driven advice for farmers and vets to choose an accurate intervention (do nothing, vaccinate, medicate, take hygienic measures, etc.).
Integrate the ranking of the burden of disease (in close collaboration with PhD2) and control options in a prototype decision support tool that will then be implemented and tested in a first pilot implementation with the end-users through stakeholder organisations (i.e. GD).
Determine the drivers and barriers for the use of the tools and improve where possible.

The preferred candidate should have a MSc degree in Veterinary epidemiology, Veterinary Medicine, Animal Sciences, or Data Sciences. The candidate has good analytical skills and experience with handling (large) datasets. Knowledge of poultry farming and experience with epidemiological methods and mechanistic disease modelling are recommended. Good command of oral and written English is a requirement. Good communication skills are essential for this interdisciplinary and international collaboration project.

More information about this position can be obtained from Prof. dr. Sjaak de Wit.

PhD 4. Developing decision support tools to be integrated in existing farm management systems for cattle farms across Europe (UGent) - Position taken

The main objective of this PhD project is to develop decision support tools for implementation in cattle production. More specifically, the objectives are:

Surveying data sources to identify which available data is most valuable in developing monitoring models and decision support tools, and help define ontologies and the methods and requirements for data access (in close collaboration with PhD1).
Identify potential end-users and stakeholders to determine their needs, willingness and associated expectations for the data-driven decision support tools to help them prioritise control and preventive measures to better manage respiratory and intestinal diseases.
Parameterise and use mechanistic disease model (INRAE, FR) and monitoring models (UCHP, DK) for dairy, veal and beef calves to providing herd specific and helpful data-driven advice for farmers and vets to choose an accurate measure (do nothing, vaccinate, medicate, take hygienic measures, etc.).
Integrate the ranking of the burden of disease (in close collaboration with PhD2) and control options in a prototype decision support tool that will then be implemented and tested in a first pilot implementation with the end-users through stakeholder organisations (i.e. Lely, GD).
The project involves both modelling for bovine respiratory disease and (neonatal) calf diarrhoea, adapted to the main production systems in the EU: dairy, beef and veal.
Determine the drivers and barriers for the use of the tools and improve where possible.

The preferred candidate should have a Master degree in bio-engineering, veterinary medicine, epidemiology, animal sciences or data sciences.

Requirements:

The candidate has experience and affinity with cattle production systems and
The candidate has experience with or is able to learn (statistical) programming and/or coding, in particular for predictive modelling purposes
Proficiency in English, both written and oral is required.
Good communication skills are essential for this interdisciplinary and international collaboration project.
The candidate can work both on her/his own, but also enjoys interaction with an interdisciplinary team and international colleagues

The student will hold a PhD position at Ghent University in strong collaboration with Utrecht University. More information about this position can be obtained from Prof. Dr. Bart Pardon.