Are you a high potential young researcher who recently obtained a PhD degree in computational biomedicine or related fields, and do you want to join our multidisciplinary team to further develop your career as an independent scientist? Do you want to push the frontier of computational modelling in medicine, and help shape the exciting new development of in silico trials? Are you keen to join our international project that aims to develop, validate, and apply the first in silico stroke trial? If you recognise yourself, we are happy to invite you to apply for this position.

We seek a scientific programmer for advanced applications in relation to Computational Biomedicine, executing on high-end massively parallel computing systems. The main focus will be on the development and maintenance of our software portfolio (for an example see our open-source cellular flow modelling toolkit: www.hemocell.eu) and to contribute to workflows in relation to in-silico clinical trials. The development tasks will include the addition of new, specialized applications of our software. These applications are often embedded in large international projects in cooperation with external partners in Sheffield, London, and Geneva. Further tasks will include supporting our scientific team to realize efficient HPC simulation solutions with these codes.

This position can give grounds to fast professional development in parallel numerical techniques, simulation methods, and application of state-of-the-art computational solutions for large-scale systems.

Project description

An exciting new emerging application of Computational Biomedicine are in-silico trials, which aim to reduce, refine, or even replace animal studies or (pre-) clinical human trials by simulating medical products or treatments on the population level.

In the INSIST project we aim to develop in-silico trials for acute ischemic stroke.

Your role will be to integrate models, as developed within the INSIST project, for virtual stroke populations, brain perfusion and metabolism, stroke treatment options (mechanical thrombectomy and thrombolysis), and statistical clinical outcome models into an overall in-silico stroke trial, to validate it on retrospective data from earlier stroke trials, and in collaboration with medical professionals and medical industry, to design and carry out two prospective in-silico stroke trials.

The candidate should have a doctoral degree in Computational Biomedicine or related disciplines. Knowledge from neurovascular disease is preferable. Experience with model integrations, workflow environments, and discrete event modelling is considered an advantage, as well as experience with modern programming languages (such as Python or C++).

This position requires strong communication skills and the capability to connect to many multidisciplinary laboratories, ranging from bioengineering and mechanical engineering, via computational science, to medical imaging, medical statistics, and neurology. You are an integrator, you are able to see the overall picture, and convince your international peers to work with you in realizing the common goal on an in-silico stroke trial. Furthermore, you should be able to work in an international multidisciplinary local team. Finally, you will also closely work together with a PhD student, and help in co-supervision.

 A temporary contract for 38 hours per week, for the duration of 24 months.

The salary, depending on relevant experience before the beginning of the employment contract, will be €2.709 tot €4.978 (scale 10 or 11) gross per month, based on 38 hours a week. These amounts are exclusive 8 % holiday allowance and 8.3% end-of-year bonus. A favorable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable. 

Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Take a look at Working at the Faculty of Science.  

University of Amsterdam

With over 5,000 employees, 30,000 students and a budget of more than 600 million euros, the University of Amsterdam (UvA) is an intellectual hub within the Netherlands. Teaching and research at the UvA are conducted within seven faculties: Humanities, Social and Behavioural Sciences, Economics and Business, Law, Science, Medicine and Dentistry. Housed on four city campuses in or near the heart of Amsterdam, where disciplines come together and interact, the faculties have close links with thousands of researchers and hundreds of institutions at home and abroad.  

The UvA’s students and employees are independent thinkers, competent rebels who dare to question dogmas and aren’t satisfied with easy answers and standard solutions. To work at the UvA is to work in an independent, creative, innovative and international climate characterised by an open atmosphere and a genuine engagement with the city of Amsterdam and society.

http://www.uva.nl/en/home

Informatics Institute

The Faculty of Science has a student body of around 6,500, as well as 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

The Computational Science Lab of the Informatics Institute aims to make dynamic complex systems tractable via computational science. We study a broad range of dynamics systems in fields ranging from biomedicine to urban, or socioeconomic systems. We also develop theory of dynamic complex systems based on concepts of information processing.

Background of the project:

Acute ischemic stroke is a devastating disease. Until 2015 the choice of treatment for stroke patients was limited to thrombolysis. In the last decennium endovascular thrombectomy (EVT), a minimally invasive procedure where the thrombus is mechanically removed by a stent-retriever, was introduced. In 2015 EVT was proven beneficial by the MRCLEAN trial and by 6 subsequent randomized clinical trials. Since then EVT has become then the standard treatment of acute ischemic stroke for occlusions of one of the proximal anterior circulation arteries. However, despite the beneficial effect of thrombectomy, still almost 2 out of 3 patients have an unfavourable outcome and become functionally dependent. Therefore, further improvement of medical products for treatment is still urgently needed, including thrombectomy device design and a new generation of improved thrombolytic therapies that also prevent incomplete microvascular reperfusion.

Because in-silico modelling allows early and fast hypothesis testing and supports trial design, the next generation clinical stroke trials can greatly benefit from in silico clinical stroke trials. This holds the promise that in silico trials enable enhanced efficacy, cost reduction, and speed up the introduction of new therapies, devices, and medication for acute ischemic stroke. With this in mind, the ‘In Silico Clinical Trials for the Treatment of Acute Ischemic stroke’ project (acronym INSIST; www.insist-h2020.eu) was initiated in 2016 and has received funding from the European Union’s Horizon 2020 research and innovation program.

The in silico clinical trials for acute ischemic stroke will consist of four main software modules. The first contains the population model to generate virtual populations of stroke patients; the second module will simulate treatment and brain tissue injury; the third module estimates outcome for each individual virtual stroke patient and the final module assembles all results and reports on the outcome.

All detailed models for these modules are under development in laboratories in Amsterdam, Rotterdam, Oxford, Galway, and Milano. In collaboration with these labs, you will coarse grain these models and include them in an event-driven coupled model that implements the in-silico stroke trial. You will validate the in-silico trial against pooled data from finalized and ongoing stroke trials. You will work with device industry and pharma, and interventional neurologists, to define and carry out two in-silico trials to test new treatment options.

http://ivi.uva.nl