This postpoc position is a part of a project on “FAIR workflows”. This is a summary of the project:
The FAIR guiding principles for data management and stewardship (FAIR = Findable, Accessible, Interoperable, Re-usable) have received significant attention, but little is known about how these principles will help researchers in their daily work. Here, we propose a novel implementation of these principles into a software suite we call the FAIR Workbench. It will enable researchers to explore, consume, and produce FAIR data in a reliable and efficient manner, including automated provenance recording and strong persistence guarantees. Such technology is urgently needed to address emerging concerns about the non-reproducibility of scientific research. We focus our attention on computational drug repositioning, an emerging field of study that aims to identify new drug uses that is faster, lower cost, and more efficient than traditional drug discovery. We explore the development of FAIR-powered workflows to overcome impediments to successful translation including unpublished data, poor quality metadata, inability to perform meta-analyses, and an overall lack of reproducibility. We will use our technology to find new drugs for cardiovascular diseases, such as heart disease and stroke, the global leaders in mortality and morbidity. As computational workflows lie at the heart of data science research, our work has broad applicability beyond the Life Science top sector.
This project is a collaboration between the Vrije Universiteit (VU) Amsterdam, Maastricht University, and the eScience Center in Amsterdam. The postdoc will work in close collaboration with the groups of Prof. Michel Dumontier (Institute of Data Science) and Prof. Harald Schmidt (Department of Pharmacology and Personalised Medicine), both at Maastricht University, and with an eScience engineer at the eScience Center, who will work on the more technical aspects of the FAIR Workbench. Another part-time postdoc will be employed at Maastricht University, who will be focussing on the application side of the project and who will be closely interacting with the postdoc at VU. In the first two years of the project, the role of VU Amsterdam is to develop FAIR-enabling methods of provenance recording and to allow for reliable and persistent linking to FAIR input/output. In year three, the developed methods are applied to the fields of drug repositioning and cardio-vascular diseases.
To fill the postdoc position for this project, we will be looking for an enthusiastic candidate with a strong motivation and the ability to proactively tackle the project’s aims. The candidates should have a PhD in computer science or a related field, have strong programming skills, and be fluent in English. Experiences with Linked Data, Semantic Web techniques, workflow modeling, Python (including iPython/Jupyter notebooks), and/or Life Science topics are an advantage.
Vrije Universiteit Amsterdam (VU) is a leading, innovative and growing university that is at the heart of society and actively contributes to new developments in teaching and research. Our university has ten faculties that span a wide range of disciplines, as well as several institutes, foundations, research centres, and support services. Its campus is located in the fastest-growing economic region in the Netherlands (the Zuidas district of Amsterdam), and provides work for over 4,500 staff and scientific education for more than 23,000 students.
Research at the Faculty of Sciences focuses on the areas of Life & Health, Networked World, Web Science, Fundamentals of Science, and Energy & Sustainability. The faculty’s teaching activities are directly linked to this excellent research. The VU Department of Computer Science is part of the Faculty of Science.
The VU Department of Computer Science has approximately 170 members, including 35 tenured staff members and 40-50 PhD students. The tenured staff members form the essential basis for the functioning of the department. A tenured staff member is required to make significant contributions to the research and education programmes, and to spend effort on specific tasks at the department level.
The VU Department of Computer Science hosts one of the leading Semantic Web research clusters worldwide. This postdoc position is part of the User-Centric Data Science group, which is part of this Semantic Web cluster and has a specific focus on semantic techniques in scientific publishing, user-centered design practices, semantic technologies for modeling users and contexts, human computation, crowdsourcing and collective intelligence. Researchers from this group have delivered key contributions to internationally renowned methodologies, frameworks and languages for knowledge engineering, intelligent user interfaces and Semantic Web technologies.