e-BioScience at the AMC

The e-Bioscience group is part of the Bioinformatics Laboratory of the Department of Clinical Epidemiology, Biostatistics and Bioinformatics of the Academic Medical Center of the University of Amsterdam.

The goal of the e-Bioscience group is to design, develop and deploy advanced technology to enable and enhance biomedical research. In particular we aim to strengthen to develop an e-Bioscience infrastructure (e-Bioinfra) based on state-of-the-art technology and concepts in order to (a) support and advance AMC research and (b) link AMC research to (inter)national e-science/GRID initiatives.

We address the following themes to develop the most appropriate infrastructure:

• User front-ends with the infrastructure, in particular usability aspects;
• Tools to facilitate computing on grids, in particular workflows;
• Tools for secure sharing of large data sets on grids;
• Interoperability, connectivity and integration of the e-BioInfra with other components of the AMC IT infrastructure;
• Security;
• Advanced system architectures and technologies.

Feel free to look futher for more information about the EBioInfra.

Background

In the past years an e-Science infrastructure was set-up at the AMC to facilitate research in medical imaging in the scope of the Medical Diagnosis and Imaging (vlemed) subprogram of the VL-e project. This infrastructure is composed of computing and storage resources of the Dutch e-Science Grid, several systems that implement services on the grid, and a user-friendly front-end that can be installed on the researcher’s desktop or laptop to access these services. Since May 2008 researchers at the AMC have successfully adopted this infrastructure to investigate methodological questions in functional MRI (neuroscience) and DTI (medical imaging) that so far were only rarely studied. Because the researchers can directly and autonomously access the advanced computing Grid resources, computing time or storage space have ceased to be a barrier to the scientific questions they want to address, leading to enhanced Bioscience (e-Bioscience). Large parts of this e-Bioscience infrastructure can be applied to genomics research, being currently also adopted for high-throughput DNA sequencing in the AMC. In addition, we have started to make the infrastructure available also for proteomics research. Both the sequencing and proteomics infrastructure activities are part of a large national programme ( NBIC BioAssist) that aims to develop common platforms for bioinformatics support.

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