Medical Bioinformatics and e-Bioscience

e-BioInfrastructure (e-BioInfra)

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.

Hardware

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.

Documentation

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!

Access

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)

• cite this paper if you have used the e-bioinfra: http://www.ncbi.nlm.nih.gov/pubmed/20371412

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: