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Speakers

Keynote speakers
Picture of Frederik Coppens
Frederik
Coppens
Picture of Michel Dumontier
Michel
Dumontier
Picture of Christine Durinx
Christine
Durinx
Picture of Patricia Palagi
Patricia
Palagi
Invited speakers
Picture of Rob Hooft
Rob
Hooft
Picture of Rafael Jimenez
Rafael
Jimenez
Picture of Marco Roos
Marco
Roos
Picture of Amnon Shvo
Amnon
Shvo
  Picture of Domenica D'Elia
Domenica
D’Elia
   


Frederik Coppens,
VIB, University of Gent, Belgium.

As deputy Head of Node and Technical Coordinator of ELIXIR Belgium, Frederik Coppens is leading the development of the Belgian ELIXIR node. He represents ELIXIR Belgium in the ELIXIR Heads of Nodes Committee, attending strategic meetings and ensuring smooth information exchange related to ELIXIR both internally within the node as towards the ELIXIR Hub.
Within ELIXIR Europe, Frederik is involved in the Plant Community and is co-chair of the Galaxy Community. The ELIXIR Plant Community focusses in the ELIXIR-EXCELERATE H2020 project on making plant phenotyping data FAIR by developing and implementing metadata (Minimal Information About a Plant Phenotyping Experiment – MIAPPE) and data access (Breeding API) standards. The Galaxy Community is active in the area of scientific workflows and aims to enable researchers to perform bioinformatics analysis workflows through a user-friendly online interface (Galaxy). For more technically advanced users, cloud-oriented technologies (e.g. BioContainers), are being developed, in which the Belgian Node also is involved.
At the VIB-UGent Center for Plant Systems Biology, Frederik Coppens is IT manager and Project Leader of the Applied Bioinformatics and Biostatistics (ABB) group. The mission of the ABB group is to enable (wetlab) scientist to perform bioinformatics and biostatistical analyses. His team provides consultancy to optimise the setup of the experiment, generation of data and analysis for biostatistics and bioinformatics in general. Moreover, solutions are foreseen for diverse NGS applications through implementation of standard workflows in Galaxy or through custom data analysis. The combination with IT manager enables optimisation of the required IT infrastructure towards the data analysis and storage needs of our researchers.

FAIR data, tools and workflows: a user perspective
The goal to move towards a more Open Science environment has inspired funders and institutes to e.g. include data management plans and open access publication into grant requirements. To also ensure reproducibility in bioinformatics, the whole data analysis chain needs to be taken into account, from input and reference data over tools and workflows to results. While this is a positive evolution, it also confronts researchers with a number of challenges. These are largely in the realm of infrastructure, therefore we need to ensure that researchers have access to tools and services that can help them meet these challenges.
In his talk, Frederik Coppens will highlight a number of challenges users have to deal with and the solutions ELIXIR is working on to enable FAIR data, tools and workflows.



Michel Dumontier,
University of Maastricht, The Netherlands.

Michel Dumontier is a Distinguished Professor of Data Science at Maastricht University. His research focuses on the development of computational methods for scalable integration and reproducible analysis of FAIR (Findable, Accessible, Interoperable and Reusable) data. His group combines semantic web technologies with effective indexing, machine learning and network analysis for drug discovery and personalized medicine. Previously at Stanford University, he now leads a new inter-faculty Institute for Data Science at Maastricht University with a focus on accelerating scientific discovery, improving health and well-being, and strengthening communities. He is a Principal Investigator for the NCATS Biomedical Data Translator and a co-Investigator for the NIH BD2K Center for Expanded Data Annotation and Retrieval (CEDAR). He is a technical lead for the FAIR (Findable, Accessible, Interoperable, Re-usable) data initiative, and is the scientific director for Bio2RDF, an open source project to generate Linked Data for the Life Sciences. He is the editor-in-chief for the IOS press journal Data Science and an associate editor for the IOS press journal Semantic Web.

Are we FAIR yet? And will it be worth it?
The FAIR Principles propose essential characteristics that all digital resources (e.g. datasets, repositories, web services) should possess to be Findable, Accessible, Interoperable, and Reusable by both humans and machines. The Principles act as a guide that researchers and data stewards should expect from contemporary digital resources, and in turn, the requirements on them when publishing their own scholarly products. As interest in, and support for the Principles has spread, the diversity of interpretations has also broadened, with some resources claiming to already “be FAIR”.
This talk will elaborate on what FAIR is, what it entails, and how we should evaluate FAIRness. I will describe new social and technological infrastructure to support the creation and evaluation of FAIR resources, and how FAIR fits into institutional, national and international efforts. Finally, I will discuss the merits of the FAIR principles (and what we ask of people) in the context of strengthening data-driven scientific inquiry.



Christine Durinx,
Swiss Institute of Bioinformatics, Switzerland.

Christine Durinx is the Associate Director of SIB Swiss Institute of Bioinformatics since 2014. She is co-lead of the ELIXIR Data Platform. The ELIXIR Data Platform has developed a process to identify European data resources that are of fundamental importance to research in the life sciences and are committed to the long term preservation of data. These resources are called ELIXIR Core Data Resources. Christine was also involved in a study on funding models to improve the long term sustainability of the data science infrastructure.
At SIB, Christine is responsible for the Communications and Training departments, the Director’s Office, and the Technology Group. Christine has a Pharmacy degree and a PhD in Pharmaceutical Sciences from the University of Antwerp, Belgium. Before joining SIB, she worked in the pharmaceutical industry for over 10 years.

ELIXIR Core Data Resources: FAIR, community and impact
The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. Central to defining this infrastructure is the identification of Core Data Resources that are of fundamental importance to the broad life sciences community. In this presentation we will describe the Core Data Resource indicators, compare them with the FAIR principles, and explain their application within ELIXIR’s sustainability strategy and science policy actions, in capacity building, life cycle management and technical actions.



Patricia Palagi,
Swiss Institute of Bioinformatics, Switzerland.

Patricia Palagi is a biologist and computer scientist by training. She joined the SIB Swiss Institute of Bioinformatics 20 years ago as a researcher in neural networks, proteomics, and bioinformatics for mass spectrometry. Since 2013 she has been leading the SIB Training group. She has a long track record of academic teaching and training in bioinformatics. She’s involved in the organisation and delivery of bioinformatics training courses, in ‘Train the Trainer’ activities, and collaborates with ELIXIR Nodes, GOBLET and international partners on several initiatives to promote training and its best practices. She is ELIXIR Switzerland Training Coordinator and co-leader of the ELIXIR Training Platform.

Challenges in adopting FAIR principles in Training
Providing bioinformatics training to help life science researchers effectively work with ELIXIR resources is ELIXIR’s key priority. The ELIXIR Training Platform is in charge of building a sustainable training infrastructure, covering training courses, training tools and resources, development of training expertise, definition of quality assurance standards and monitoring of quality indicators. TeSS, the ELIXIR training portal which aggregates course events and materials, was designed in compliance with Bioschemas and FAIRsharing recommendations and adopting FAIRE principles. ‘Train the Trainers’ courses and several ELIXIR specific courses were designed to promote FAIRness and open access in sciences principles. In this presentation, we will talk about these and other measures implemented by ELIXIR to ensure training is FAIR, to ensure the ELIXIR community is aware of FAIR principles and is trained to adopt them. The training challenges and issues related to the adoption of FAIR principles and to the implementation of FAIR data, tools and platforms will also be elaborated.



Rob Hooft,
Dutch Techcentre for Life Sciences – DTLS, The Netherlands.

Rob Hooft was educated as a structural chemist at Utrecht University under Professor Jan Kroon. He did his PhD studies on the subject of structure-activity relationships of sweet tasting compounds. He spent 4 years at the EMBL in Heidelberg where he developed tools to verify the quality of protein structures in the group of Gert Vriend and Chris Sander.
He joined the company Nonius in 1997 where he developed application software for a diffraction system with a CCD detector. When Nonius and Bruker AXS merged in 2001, Rob led the team of developers for the company in Delft. This team developed components and systems for X-ray diffraction analysis.
When Bruker AXS has stopped their R&D in the Netherlands, Rob moved back to the academic world and joined the Netherlands center for Bioinformatics, NBIC, as CTO for the service-directed program. Via a two year excursion to the Netherlands eScience Center from where he ran the data program of the Dutch Techcenter for Life Sciences (DTL), he is now working for DTL itself managing the Dutch tasks in the European ELIXIR infrastructure for life science data. As part of these roles, Rob has been building up a body of knowledge on FAIR research data stewardship since early 2014.

A FAIR approach to Research Data Stewardship and Data Stewardship Planning
The call for open and reproducible science has led to a widespread implementation of “Data Managemant Plans”. However, many researchers are not convinced how Data Management and Data Management Planning will benefit their work. And in many areas of e.g. privacy sensitive data, there is generic resistance against Open data. In this talk I will show our approach for what we call “FAIR Data Stewardship”: A form of data management that has as its ultimate goal to make data as Reusable as possible for a period that extends as long as possible after the project finishes. I will give an impression of the breath of expertise needed to do this, will show how this benefits the researcher applying it, and will also show how a tool currently under development in ELIXIR can help to bring researchers and the right data stewardship experts together. I will refer to ongoing training activities in this area, and also show how the experts in the conference can contribute to the FAIR Data stewardship expertise network.



Rafael Jimenez,
ELIXIR Europe, Cambridge, United Kingdom.

Rafael Jimenez is the Chief Data Architect at ELIXIR. He has an active role in the technical design, coordination and implementation of the ELIXIR data infrastructure. He joined ELIXIR after four years at EMBL-EBI as a software engineer and technical lead in the Proteomics Services team. He is specialised in the coordination and management of bioinformatics services, and is interested in topics relating to data infrastructure, data integration, data federation, data visualisation and software development best practices. Rafael has experience coordinating technical projects, developing technical strategies, leading software development and managing community groups. He obtained his MSc in Molecular Biology in Spain and his MSc in Computer Science in South Africa.

FAIR data and EOSC (European Open Science Cloud): Strategy for finding and accessing datasets at EOSC
The EOSCpilot project has produced a first draft of the strategy and recommendations to help users and services to find and access datasets across several scientific disciplines. In this talk we will introduce the strategy, recommendations as well as the principles driving this work. We will also explain how this strategy contributes to make data FAIR, how data providers in the life sciences can contribute and how ELIXIR plans to implement this strategy.



Marco Roos,
Leiden University Medical Centre – LUMC, The Netherlands.

Marco Roos is assistant professor and group leader of the Biosemantics group of the Leiden University Medical Centre (Human Genetics department). His research focus is on making state-of-the-art computer science applicable to enhance biomedical research (e-Science), particularly the application of computational knowledge discovery and linked data techniques to address translational research challenges of rare human diseases.
He started his career studying the role of the genome and chromatin in the functioning of the cell, which is still one of his interests. After including computer science in his MSc on molecular and cellular biology, he worked as a multidisciplinary researcher in research groups in both life science and computer science research groups. He now leads the research, development and application of knowledge discovery of the Biosemantics group. The group that includes professor Barend Mons, is known for co-founding and advocating the FAIR data principles. At an international level, Marco is focused on the implementation of FAIR principles to create a powerful substrate and world-wide robust infrastructure for knowledge discovery across distributed rare disease data resources. He co-leads the rare disease user community of the European life science data infrastructure ELIXIR, and the cross-project rare disease data linkage plan and linked data and ontology task force. He also leads the initiative to organise a Global Open FAIR implementation network for rare diseases. GO FAIR implementation networks are a mechanism to implement the European Open Science Cloud.

From rare to FAIR data in the rare disease community
Access to care and providing treatment to patients of rare diseases (RD) constitute major challenges for society. Around 7% of the population suffers from one of over 6,000 known RDs, each of which has low to extremely low prevalence. Data are sparse, but clinicians, patients and researchers are highly motivated to collect data. This results in data that are heterogeneous and highly fragmented across organisations and nations. Sharing is hampered by ethical and legal restrictions and an increased risk of patient identification. As in other areas, siloeing of data and biosample collections is a problem, but the need to be able to retrieve and analyse information across resources is exceptionally high for RDs. In fact, in order to reach the goals that the RD community has set itself, the efficiency of cross-resource information retrieval and analysis needs to increase manyfold in the coming years.
Machine readability will have to play a major role in that. Data linking by ontologies, and more recently the FAIR data principles, have therefore acquired a lot of interest. In fact, workshops in the RD domain were instrumental for developing tools and the FAIR guiding principles for managing scientific data. Initiated by RD-Connect, and with support of ELIXIR, BBMRI-ERIC, FAIR-related projects in the Netherlands, and RD stakeholders, we have started to build infrastructure (tools, best practice protocols, training, project planning, data steward networks) for RD resources to become linkable and FAIR at source (e.g. RD patient registry at a hospital) and down to the data element level.
I present the journey we are taking, how we involve the community, which elements we use to address which aspects of FAIR, and challenges ahead. Our experiences make clear that FAIRification is non-trivial and by definition a multidisciplinary, community effort. We observe that many technical, management, and social challenges have to be addressed at the same time, but also that a strong community can do this. We observe the RD community working towards converging on standards at different levels, engaging in the refinement of FAIR tooling, and we see the emergence of data steward networks and FAIRification services.



Amnon Shvo (Shabo),
The International Academy of Health Sciences Informatics.

Amnon Shabo (Shvo), PhD, works in Philips as a health informatics specialist. He worked in IBM Research (2000-2014) where he co-founded and chaired the Medical Informatics Community and headed the IBM worldwide program on healthcare & Life Sciences standards. Amnon established and chairs two professional working groups: (1) the IMIA Working Group on Health Record Banking and (2) the EFMI Working Group on Translational Health Informatics.
Amnon has been leading key standardization activities: he established and co-chairs the HL7 Clinical Genomics Work Group and is a co-editor of the Clinical Document Architecture (CDA), Continuity of Care Document (CCD), the Family Health History (Pedigree) and the Genetic Testing Report (GTR) standards. Amnon specializes in longitudinal and cross-institutional Electronic Health Records and is a pioneer of the Independent Health Record Banks vision. In the early nighties, Amnon founded a startup with Hadassah Medical Organization in the area of patient simulations. In his postdoc studies at Georgia tech, he specialized in case-bases reasoning.

Paradigm shifts in health informatics needed for leveraging FAIR data environments
Current attempts to personalize health care are mostly about classifying a patient to a handful number of predefined population groups, for which evidence exists on best practices.
In order to move closer to precision medicine for an individual patient, three paradigm shifts are proposed (building on FAIR data):

  1. develop a compositional health information language supporting translational medicine, and phase out usage-specific standards that are rigid, limited, inconsistent and constantly changing,
  2. add case-based reasoning to the decision support techniques and use it to further personalize results of rule-based techniques; broaden the case scope to be the lifelong health history of the individual,
  3. integrate and sustain lifelong health records via ‘independent health record banks’ – new players that are designated as the sole health record keepers.


Domenica D’Elia,
CNR-ITB, Bari, Italy.

Domenica D’Elia is a molecular biologist working in the field of Bioinformatics since 1996. She holds a PhD in Biochemistry and Molecular Biology from the University of Bari. After few years working at the University on the biogenesis of mitochondria, she moved to the Italian National Research Council Institute for Biomedical Technologies (CNR-ITB), where she has been working as a Project and Team Coordinator for the development of specialised biological databases. In this role, she has led and contributed to the development of diverse databases, bioinformatics integrated platforms and of data mining tools. Nominated as representative of the Italian National Node of EMBnet – The Global Bioinformatics Network in 2006, she has been working inside the network in different roles up to her election as Chair of EMBnet in 2016.
As former Chair (2010-2015) of the EMBnet “Publicity and Public Relationships Project Committed”, Domenica assisted and contributed to the establishment of GOBLET, the “Global Organisation for Bioinformatics Learning, Education & Training”, of which she is presently a member. She has also contributed to the activities of the Steering Committee of the Bioinformatics Italian Society (BITS) in 2010-2012 and collaborate to the actions of the Society as an Ordinary member since its foundation.
At CNR-ITB, she is Project Leader of a research line on the “Effects of Exogenous Plant miRNAs on the Expression of Human Genes Involved in Ageing-Related Diseases” (SCKT – Flagship InterOmics Project), and is collaborating with the “Research Council for the agricultural research and the analysis of agricultural economy” (CREA) on a nutrigenomics study that investigates the effect of a local table grape variety on cell homeostasis and human health.
Starting from January 2016 she is a member of the Management Committee of the COST Action CHARME ”Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research” (CA15110) and Chair of the CHARME WG4: “Development of a strategic dissemination action”.

Standards and SOP implementation in the life-sciences research: a snapshot from the COST Action CHARME
In a world where the biological and clinical research relay almost entirely on new and advanced high-throughput technologies and sophisticated approaches to omics data integration, the quality, reliability and format of data represents the most valuable features to be ensured. To answer to this pressing need, in 2005 the Research Data Management (RDM) initiative introduced a new set of principles for data management services. Following their principles, data should be FAIR – Findable, Accessible, Interoperable and Reusable. However, applying the FAIR data principles mainly addresses the metadata levels and does not necessarily take into account the quality of the source datasets, an essential prerequisite of good research. Generating data according to standards, using Standard Operating Procedures (SOPs) and implementing efficient Data Management Plans (DMP), by also hosting data on sustainable infrastructures are crucial steps forward a safe and reliable way to do research.
Harmonising standardisation strategies to increase the efficiency and competitiveness of European life-science research (CHARME), is an 4-year Action founded through COST (European Cooperation in Science and Technology) which addresses two main challenges: the sensibilization of the European scientific community and of different stakeholders around the theme of standards, and the unification of efforts of different initiatives toward the implementation of a common and efficient strategy to promote good practices at all levels of the data production and analysis processes.
In her talk, Domenica D’Elia will present CHARME by underlining the scenario in which it moves forward and actions that the scientific community is called to support for a global implementation of standards and SOPs in the life-sciences research.




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