Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

The e-Bioinfra Gateway (e-Bioinfra Gateway) is a web application that provides facilitated access to the Dutch Grid infrastructure for researchers that need to analyse large data collections with complex or compute-intensive methods. The researcher just needs to follow some steps on a web interface using any web browser. The web link is http://www.ebioscience.amc.nl/ebioinfragateway/

The following steps are needed to use the e-Bioinfra Gateway:

The e-Bioinfra Gateway is developed and maintained by the e-BioScience group of the Bioinformatics Laboratory of the AMC, Department of Epidemiology, Biostatistics and Bioinformatics (KEBB). This research is supported by the BiGGrid project (NWO funding), the COMMIT project "e-Biobanking with imaging for healthcare", and the AMC ICT Innovation Fund.

For more information please contact us.

Registration

In order to use the e-BioinfraGateway, users should register as follows:

  1. 1 Provide the needed information on the registration web page, and agree to the terms and conditions.
  2. Fill out the intended usage form: here.
  3. Our administration will inform you via email as soon as your account is activated.

NOTE:

Your account includes access privileges to the e-BioinfraGateway website and to the data staging machine, to which the data should be uploaded. The passwords to both accounts are the same.

registration-form.PNG

Experiment Setup

In the documentation pages of each experiment type, there is usually a section which describes the supported input data and any additional step to prepare the input data. Please make sure that you read that section carefully and you provide the input data exactly as described in that section.

In addition, please note that we highly recommend to the users of the e-BioinfraGateway to start their data analysis with a small set of data (e.g., 2 subjects) and confirm the results before proceeding with the complete data set analysis.

Data Transport

The research data to be analysed on the Grid needs to be transferred to grid storage outside the AMC network in a secure manner. This is done with the aid of an intermediary storage server at the AMC, called data staging machine. Each researcher has a private space that can hold data for a limited time (1-2 weeks). All data copied into this machine are automatically transported to the Grid storage. Likewise, all results generated by calculations executed on the Grid are copied back to the data staging machine.

Files can be copied to/from this space by the researcher using regular ftp client programs such as WinSCP, FireFTP or FileZilla. For the examples on the user documentation we are using FireFTP. If you don't have administrative rights on your windows / AMC-OpenPC machine you can use the .ZIP version of FileZilla, which does not require installation (just unzip and use).

Important Notes:

  • Please avoid using "." (except the final dot before extension), and "spaces" in the file name. So "subject.001.nii" and "subject 001.nii" are not good but "subject-001.nii" and "subject_001.nii" and "subject-001.tar.gz" are good.
  • File names should be between 1 and 50 charachters (and not longer).
  • Please make sure that your input data is prepared according to each experiment requirements.
  • You have to select individual files (and not directories) in the 'input selection' page of experiment. (We suggest using a flat directory structure for input data but if you prefer to store your input files in sub-folders then you need to provide 'custom input data directory' on 'upload' page.)
  • Issues with the Internet Explorer (on AMC OpenPCs): Please use a real web browser (i.e., Mozilla Firefox). Unfortunately Internet Explorer is unable to detect redirects to SFTP links that are used for accessing the files.

Applications

Application Name Function Documentation
DTI Preprocessing preprocessing of the DTI Atlas data analysis DTI Preprocessing on the e-BioinfraGateway User Documentation
DTI Atlas registration of large collections of DTI images DTI Atlas on the e-BioinfraGateway User Documentation
Freesurfer brain surface segmentation from MRI images Freesurfer on the e-BioinfraGateway User Documentation
BLAST alignment of DNA sequence data with a given database BLAST on the e-BioinfraGateway User Documentation
T-B Cell Variation   T-B Cell Variation User Documentation
Genome Compare counts and clusters homologous genes to find related strains Genome Compare User Documentation

Publications

  • S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Springer Journal of Grid Computing.
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. Luyf, A. van Kampen, and S. Olabarriaga. Front-ends to Biomedical Data Analysis on Grids. In Proceedings of HealthGrid 2011, Bristol, UK, 2011. PDF
Topic attachments
ISorted ascending Attachment Action Size Date Who Comment
PDFpdf ebioinfragate.pdf manage 244.4 K 2011-08-01 - 13:22 ShayanShahand healthgrid 2011 paper
Topic revision: r41 - 2013-05-06 - ShayanShahand
 
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