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Netherlands Bioinformatics Centre

Netherlands Bioinformatics Centre

2 Projects, page 1 of 1
  • Funder: Netherlands Organisation for Scientific Research (NWO) Project Code: 176.010.2005.009

    Many scientific disciplines are presently undergoing technological revolutions that lead to a common challenge: managing a distributed data explosion. Detectors, medical imaging instruments, micro-arrays, and multi-sensor instruments are producing amounts of data that are rapidly exceeding the capacities of their current local data storage and computing environments. In many cases these ?exploding data? are distributed from the very start, being produced by different research groups or distributed sensor networks. Consider examples like genome and protein analysis data produced by many research labs in the world, biobanks containing patient data from a variety of hospitals, biodiversity data collected at the banks of the river Waal, historical archives and text corpora in many different places. Combining these datasets allows for completely new forms of research. Moreover, experiments generating petabytes of data per year, such as LOFAR in radio-astronomy and CERN in particle physics, need more data processing power than ever can be located in a single facility, with data utilized by researchers all over the world. From an ICT perspective, these data have similar properties: all require reliable storage, comprehensive archiving, secure coupling and sharing. We propose to build and roll out a nation-wide grid-based e-Science infrastructure, BIG GRID, that strengthens the international position of the Netherlands in many scientific areas. BIG GRID encompasses data storage facilities and data processing services, enabled by grid services, for a requested budget of 30 M€ over a four-year period. The science case for this proposal is the integral of many different science cases, reflecting the broad scientific community base. The realization of BIG GRID is crucial to the success and continuity of many Dutch research communities, covering important areas such as life sciences, astronomy, particle physics, meteorology, and climate research, water management, to name just a few. However, the very nature of the new infrastructure, a multidimensional collaboration enabler and accelerator, allows for direct participation of also social sciences, humanities, and even addresses communities in administrative domains, like digital academic repositories. One basic ingredient for the proposed infrastructure is the network. The Netherlands are already in an excellent position, due to the world-class network services provided by SURFnet, the upgrade of which has been secured from GigaPort-NG project. BIG GRID provides opportunities for enhanced international visibility. Dutch participation in international generic grid developments is already prominent (in flagship projects like EGEE and DEISA) and are on a national scale very well covered by the VL-e project. Coordinated by the Netherlands Genomics Initiative, NBIC is the key player for enabling informatics methodology for life sciences. While the Netherlands is a leading player in the development of the grid, and has considerable expertise in bio-informatics, distributed sensors networks, and particle physics, the large-scale infrastructure to fully exploit this leading position is missing. The purpose of this proposal is to realize a science-wide national grid infrastructure. This puts the Netherlands at the forefront of grid developments, enabling many national ambitions. It enhances the excellent position of Dutch academic hospitals in patient data collections using the grid for biobanking. It enables major advances in drug discovery through combining data and through availability of massive compute resources for modelling. It allows industrial research labs, such as Philips, to both contribute to and profit from the available resources for engineering sciences. It positions LOFAR as the European centre for serving a variety of scientific communities using LOFAR data and the Netherlands as one of the Tier-1 sites for CERN?s LHC experiments. This proposal is a collaborative effort of NCF, NBIC and NIKHEF.

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  • Funder: Netherlands Organisation for Scientific Research (NWO) Project Code: 184.033.111

    Biobanks are collections of samples, data and images of individuals taken at different stages of their lives, either when they are ill or when they are healthy. They have agreed to take part in health-checks or population health studies. Biobanks are a vital source of information for fundamental and translational biomedical research aimed at the development of better predictive, preventive, personalized and participatory (‘4P’) health care. Historically, Dutch biobanks were developed independently, based on, for example, research interest, local or regional activities, or clinical discipline. Today, in the era of genomics and modern imaging, there is an urgent need to connect the extremely valuable information held in biobanks through a large-scale, standardized biobank infrastructure to avoid redundancy, create efficient research workflows, streamline and facilitate data access, and optimally link various sorts of data. Such a national biobank infrastructure will enable efficient health monitoring, validation of life style interventions and other ways to prevent disease, deliver better diagnostics and therapeutics, and expand the leading position of the Netherlands in international biomedical research. A large-scale biobank infrastructure is also essential to help generate the ‘evidence base’ required by registration and reimbursement authorities to assess the impact/quality/cost-benefit ratio of screening programmes, medications and treatments. The Netherlands is currently one of the world-leaders in biobanking with respect to both the number of its biobanks and the amount of material held by them, and in terms of its internationally knowledged expertise. In recent years, several important nationwide initiatives have been undertaken to organize and professionalize biobanking, including the String of Pearls Initiative (PSI), the European Population Imaging Infrastructure (EPI2), and the Translational Research IT project of the Centre for Translational Molecular Medicine (CTMM-TraIT). BBMRI-NL (Biobanking and BioMolecular Research Infrastructure Netherlands) was established to align, connect, complement and enrich biobanks, and to lay the groundwork for a robust national biobank facility. The first phase of BBMRI-NL (BBMRI-NL1.0; 2009-present) was highly successful and united 193 Dutch biobanks (population and clinical), jointly containing materials and data from >900,000 individuals, ~13 million biobanked samples, and a wide spectrum of accessory data. It lay the foundation for a well-organized national biobanking infrastructure for Dutch biomedical research. BBMRI-NL is the Dutch hub of the BBMRI ERIC (BBMRI European Research Infrastructure Consortium) and is closely aligned with major European initiatives and ‘Grand Challenges’ in the European Framework programme (e.g. Healthy Aging in Horizon 2020), and national initiatives, like the Life Sciences & Health ‘top sector’. With the recent complementary initiatives of EPI2 and CTMM-TraIT and major extra funding for data collection in specific sub-populations (notably the ‘Deltaplan Dementia’), the time has come to make the next decisive step towards a truly nationally integrated ‘NL Biobank Research Facility’ with BBMRI-NL2.0. In the future, biobanking will increasingly be integrated with health care. BBMRI-NL 2.0 will allow biomedical researchers to contribute to ‘4P’ medicine by linking diverse data sets through coordinated access to biomedical resources, technologies, standards and know-how, supported with cutting-edge IT systems and tools, and by providing tools for the standardization and harmonization of data, and its long-term storage. BBMRI-NL2.0 presents a unique opportunity to bring together Dutch biobank and imaging collections that are among the largest in Europe, building on proven success and extensive expertise in the compilation and analysis of such extensive datasets. BBMRI-NL2.0 will enable fully integrated access for research on how genetic and environmental factors contribute to disease. The research results from BBMRI-NL2.0 will drive new and improved ways to diagnose and predict disease, and highlight factors critical to disease prevention, healthy ageing or optimal development, and thus to the quality of life. It will cement the Netherlands’ leading position in biobank-based biomedical research. The envisioned NL-Biobank, with its content ranging from genes, molecules and images to their clinical cognate, will provide a unique repository of integrated data that optimally prepares the Netherlands for the challenges of Horizon 2020 and makes BBMRI-NL2.0 a highly visible and attractive partner for international collaborations.

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