The e-BioScience Infrastructure (e-BioInfra) was initially developed for medical image analysis applications as part of the Medical Diagnosis and Imaging
subprogram of the Virtual Laboratory for e-Science project. Originally it was coined the "VLEMED" platform. It is currently composed of:
- The Dutch e-Science Grid provided by the BiGGrid project.
- Several systems that implement services on the grid (for example, workflow management, provenance)
- Various user interfaces, including web, VBrowser and command-line.
For more details see the e-BioInfra advanced page
The hardware components of the e-BioInfra are distributed. The acquisition devices (e.g., MRI scanner, Sequencer) are located at the AMC network, and the computing and storage resources are located in distributed sites connected to the Dutch e-Science Grid (currently 11 sites). Users located anywhere (e.g., at the hospital, university, home) can access the system to manipulate data and run workflows from their own workstations.
Software and Services
The communication with the grid resources is intermediated by services that run on the e-BioInfra server. Most of them are activated transparently and automatically via the VBrowser. The main software components of the infrastructure are illustrated in the figure. The components in blue are developed and/or maintained by the e-BioScience team.
The easiest way is to use the web interface
, which provides access to predefined programs (Note: currently available only for selected neuroimaging and DNA sequencing applications).
For more flexible usage a researcher needs to take some steps that are explained in more detailed at the GettingStarted
guide. Check also the documentation
We are happy to help you get started, please contact us
Before publishing work that have used the e-bioinfra facilities, please contact us
All publications based on generated (indirectly) with the help of computing performed in the ebioinfra need to:
- cite this paper if you have used the web interface of the e-Bioinfra Gateway:
S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing.
Journal of Grid Computing. December 2012, Volume 10, Issue 4, pp 725-742 (doi
Olabarriaga SD, Glatard T, de Boer PT. A virtual laboratory for medical image analysis. IEEE Trans Inf Technol Biomed. 2010 Jul;14(4):979-85. Epub 2010 Apr 5.
- include the following text in the acknowledgements:
This work performed computations using the e-bioinfra platform developed at the e-bioscience group of the Bioinformatics Laboratory of the AMC, using resources of the Dutch e-Science Grid, BiGGrid project, which is financially supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research, NWO).
If you have used the e-Bioinfra services and made special requests and/or received help for your data analysis please contact us for further arrangements.
- Report to us about any publications. We need to regularly inform NWO about the usage of the Dutch grid from the e-bioinfra platform.