Medical Bioinformatics and e-Bioscience

e-BioScience Web

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News People EBioInfra Research Overview Projects Publications Tools & Services Getting Started Documentation e-BioInfra Gateway VBrowser MOTEUR Training & Education Contact	Welcome to the website of the e-Bioscience research line of the Bioinformatics Laboratory of the Department of Clinical Epidemiology, Biostatistics and Bioinformatics of the Academic Medical Center of the University of Amsterdam. The mission of the e-Bioscience research is to improve and increase the capacity, scope and quality of biomedical research performed at the AMC. We serve as bridge between biomedical and clinical researchers, who have data analysis problems that cannot be tacked by their current tools, and the vast amount to expertise in information and computation sciences existing outside the AMC. Together we define use cases that are implemented as a common effort. As basic platform we adopt the e-infrastructure for biomedical research (e-Bioinfra), using state-of-the-art concepts and technology. In this process we address the following main themes: Worfklow technology to perform complex scientific experiments on distributed infrastructures (e.g. grid, clusters and cloud); User front-ends with the infrastructure, in particular web interfaces (so called "science gateways"; Distributed systems architectures and technologies. Interoperability, connectivity and integration of the e-BioInfra with other components of the AMC IT infrastructure; Security; Data management, including provenance See also the an overview and team members. The activities of the e-bioscience group are funded by various projects and organizations.

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About

Welcome to the website of the e-Bioscience research line of the Bioinformatics Laboratory of the Department of Clinical Epidemiology, Biostatistics and Bioinformatics of the Academic Medical Center of the University of Amsterdam.

The mission of the e-Bioscience research is to improve and increase the capacity, scope and quality of biomedical research performed at the AMC. We serve as bridge between biomedical and clinical researchers, who have data analysis problems that cannot be tacked by their current tools, and the vast amount to expertise in information and computation sciences existing outside the AMC. Together we define use cases that are implemented as a common effort.

As basic platform we adopt the e-infrastructure for biomedical research (e-Bioinfra), using state-of-the-art concepts and technology. In this process we address the following main themes:

Worfklow technology to perform complex scientific experiments on distributed infrastructures (e.g. grid, clusters and cloud);
User front-ends with the infrastructure, in particular web interfaces (so called "science gateways";
Distributed systems architectures and technologies.
Interoperability, connectivity and integration of the e-BioInfra with other components of the AMC IT infrastructure;
Security;
Data management, including provenance

See also the an overview and team members.

The activities of the e-bioscience group are funded by various projects and organizations.

History
During the VL-e project (2004-2009) an e-Science platform was set-up at the AMC to facilitate research in medical imaging by the Medical Diagnosis and Imaging (vlemed) subprogram. This platform contains computing and storage resources of the Dutch e-Science Grid, several web-based systems that implement services on the grid, and it can be accessed from a user-friendly front-end. Since May 2008 researchers at the AMC have successfully adopted this platform in various research areas, including medical imaging (neuroscience) and genomics (next generation sequencing). The data analysis "services" developed on top of this platform can be used directly by the biomedical researchers from a web interface. 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, enabling and enhancing Bioscience research (e-Bioscience).

History

During the VL-e project (2004-2009) an e-Science platform was set-up at the AMC to facilitate research in medical imaging by the Medical Diagnosis and Imaging (vlemed) subprogram. This platform contains computing and storage resources of the Dutch e-Science Grid, several web-based systems that implement services on the grid, and it can be accessed from a user-friendly front-end. Since May 2008 researchers at the AMC have successfully adopted this platform in various research areas, including medical imaging (neuroscience) and genomics (next generation sequencing). The data analysis "services" developed on top of this platform can be used directly by the biomedical researchers from a web interface. 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, enabling and enhancing Bioscience research (e-Bioscience).

Topic revision: r74 - 2013-05-23 - SilviaOlabarriaga