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SURFsara

Contact Details

SURFsara

Science Park 140, 1098 XG Amsterdam

www.surfsara.nl

Dr. I.M.A. Nooren

0031 (0)20 5923000

Hotel Description

SURFsara supports research in the Netherlands by development and deployment of state of the art high performance computing (HPC) and data infrastructure services and expertise. This includes grid and cloud computing, data storage, visualization, networking and e-science. SURFsara works closely together with the life science academic community and industry. Engineering and technology development is based on the needs of end users. Throughout the years, a life science e-infrastructure community has been set up by a collaborative project by BiG Grid (NWO/NCF, Nikhef), NBIC and SURFsara (e-BioGrid). The life science and health research sector is becoming increasingly data-intensive, e.g. DNA analyses of entire populations or ecosystems. Working with Big Data requires high standards in terms of transport, storage and – most importantly – processing. SURFsara tailors its services to the processing of growing data volumes. SURFsara accommodates a specific life science support team with broad and profound expertise in life science research to enable effective life science e-infrastructure support.

• Data and network services – We ensure that data can be easily and securely stored, made accessible and shared. Researchers can use bandwidth on demand when transporting large amounts of data between various locations. This service is provided in collaboration with SURFnet.

• Compute services – We offer a range of compute solutions. HPC Cloud typically contributes to the needs of bioinformaticians for high performance computing with a highlevel of flexibility and ownership. It allows researchers to run their own software either on more machines or on larger machines than they would normally have available themselves. Cluster and supercomputing offer high compute and memory capacity in a serviced environment and applies to a variety of life science use cases. Distributed grid computing is typically used in large-scale population studies using e.g. next-generation sequencing technology. It provides access to the largest computational resource available in the Netherlands with more than 10.000 compute cores. The Life Science Grid is especially designed for life scientists wishing to use powerful compute facilities on site, with the opportunity to share data throughout the country using lightpath network connectivity. Hadoop is an innovative compute solution that is often used for unstructured data research such as text mining. Compute job management systems, webportals and workflow solutions provide access to SURFsara’s compute services for a range of bioinformatics analyses, e.g the Life Science Grid portal and the Galaxy workflow engine.

• Visualization services – Visualization services (SURFsara, NLeSC) are available for high-resolution visualization that can be remotely controlled, allowing users to access major visualization and computing power when their own workstation has limited capacity.

Bioinformatics
Public
  • Next-generation sequencing
  • Genome-wide association studies
  • Genome analysis
  • Metagenomics
  • Medical imaging

Expertise and Track Record

The capability SURFsara is unique in the Netherlands as we operate at the front-end of innovative solutions, creating state-of the art technology. SURFsara provides the national e-infrastructure for research institutes in the Netherlands.

Genome analysis and imputation, BBMRI consortium: This research focuses on the analysis of 750 human genomes, connecting genotype changes to differences in phenotype. Estimating genetic variants based on data collected in genome-wide association studies combined with whole genome NGS datasets were run on the grid infrastructure, the life science grid. These applications are very data and computationally intense. They use a pilot job framework developed within the group itself called RITE. SURFsara’s hardware resources and expertise played an important role in building the e-infrastructure for this BBMRI subproject.

Medical imaging, AMC: The promise of extracting objective information to characterize disease (e.g. biomarkers of disease) even before it becomes symptomatic and using this information to produce patient-specific treatment (drug development) makes modern biomedical research a scientific field that is both data-intensive (vast amounts of data, heterogenous, distributed) and compute-intensive (sophisticated  analysis and simulation methods). The Life Science Grid has offered an infrastructure for scientists within the BioMed virtual Grid organisation to target these challenges.

Comparative proteomics, TU Delft: This research involves pattern recognition and machine learning in establishing and modelling protein networks. Typically, running a number of algorithms that need to be run across a variety of datasets, requires many millions of jobs which all have a limited input set and very small outputs (in the KB range). These outputs are saved to the pilot job system itself (in this case PiCaS) as this data cannot efficiently be stored on a SRM. Run times for these applications are in the order of a few hundred thousand core hours per experiment. SURFsara provided its expertise and hardware resources to make this project to a success.

Systems biology. NCSB, CWI: This Netherlands Consortium for Systems Biology (NCSB) project requires an upscale of simulations of populations of metabolizing bacteria, that are used to study behavior and evolution of gut microbiota. In silico simulation models of the gut microbiota aim to uncover fundamental principles of intestinal microbial organization and its relation to health and diet of the host. We will use this VO playground project to set up a WS-VLAM infrastructure supporting our simulation system and to perform some initial simulations with it. As a first goal we aim at identifying parameter regions that support the coexistence of multiple bacterial species. This project is in a pilot stage in order to collaboratively set up an e-infrastructure for this life science research use case.

  • Services and tools are accessible via SURFsara websites and wiki’s. See https://www.surfsara.nl/systems, and https://www.surfsara.nl/services, and references therein. Life science specific products include: http://galaxy.nbic.nl https://grid.sara.nl/wiki/index.php/Life_Science_Grid_portal https://www.surfsara.nl/project/life-science-grid

The services are offered under the “flag” of e-Infra (SURFsara, Groningen University,
and NIKHEF), it is run by SURFsara. SURFsara is part of SURF.

SURFsara works closely together with NBIC, NLeSC and the life science community
including UMCs, and is involved in a range of national and international
projects such as BBMRI and TraIT. As a member of the EGI ELIXIR virtual team,
as well as being partner in several EU projects, we share our expertise to
build EU federated e-infrastructure solutions.

Hotel Characteristics

  • Services and tools are accessible via SURFsara websites and wiki’s. See https://www.surfsara.nl/systems, and https://www.surfsara.nl/services, and references therein. Life science specific products include: http://galaxy.nbic.nl https://grid.sara.nl/wiki/index.php/Life_Science_Grid_portal https://www.surfsara.nl/project/life-science-grid