Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• 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.

• 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.

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

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

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Publications

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• Register
• Prepare data to be transported to the grid
• Run the application

Registration

Publications

• 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

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• Prepare data to be transported to the grid
• Run the application
  • DTI Preprocessing: preprocessing of the DTI Atlas data analysis

• • DTI Atlas: registration of large collections of DTI images
  • Freesurfer: brain surface segmentation
  • BLAST: alignment of DNA sequence data with a given database

For more information please contact us.

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• 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.
• 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.)

Applications

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• Register

• Run the application
  • DTI Preprocessing: preprocessing of the DTI Atlas data analysis
  • DTI Atlas: registration of large collections of DTI images

Experiment Setup

• 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.
• 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.)

Applications

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• 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
• S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Submitted.

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Publication

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Important Notes:

• 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.)

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Publication

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Data Transport

Publication

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

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 a 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 this version of FileZilla, which does not require installation (i.e., unzip and use).

Applications

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• Register

Experiment Setup

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Publication

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• • Freesurfer: brain surface segmentation
  • BLAST: alignment of DNA sequence data with a given database
  • T-B Cell Variation:

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 a 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.

Publication

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Data Transport

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

• Register
• Prepare data to be transported to the grid
• Run the application

• • DTI Atlas: registration of large collections of DTI images
  • Freesurfer: brain surface segmentation
  • BLAST: alignment of DNA sequence data with a given database

Applications

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Applications

e-BioinfraGateway

The e-Bioinfra Gateway (e-bioinfragateway) 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://orange.ebioscience.amc.nl/ebioinfragateway/

e-BioinfraGateway

• Register
• Prepare data to be transported to the grid
• Run the application

• • DTI Atlas: registration of large collections of DTI images
  • Freesurfer: brain surface segmentation
  • BLAST: alignment of DNA sequence data with a given database

e-BioinfraGateway

• Register
• Prepare data to be transported to the grid
• Run the application
  • DTI Atlas: registration of large collections of DTI images
  • Freesurfer: brain surface segmentation

Data Transport

Applications

e-BioinfraGate

• Register

e-BioinfraGate

Applications

e-BioinfraGate

• • DTI Atlas: registration of large collections of DTI images
  • Freesurfer: brain surface segmentation

Registration

Applications

e-BioinfraGate

Registration

Registration

e-BioinfraGate User Documentation

• • Freesurfer

Registration

In order to use the e-BioinfraGate, users should register like the following: 1 Provide the needed information on the registration web page, and agree to the terms and condition. Our administration will inform you via email as soon as your account is activated. Your account includes access privileges to the e-BioinfraGate website and to the staging machine, to which the data should be uploaded. The passwords to both accounts are the same. The "data staging machine" is a temporary data storage, which is inside the AMC and can be accessed (only from the AMC network) via a ftp client program like winscp, fireftp. For the examples on these user documentations we are using fireftp.

Applications

e-BioinfraGate User Documentation

The e-Bioinfra Gateway (e-bioinfragate) is a web application and can be found at http://orange.ebioscience.amc.nl/ebioinfragate/

Registration

In order to use the e-BioinfraGate, users should register like the following: 1 Provide the needed information on the registration web page, and agree to the terms and condition. Our administration will inform you via email as soon as your account is activated. Your account includes access privileges to the e-BioinfraGate website and to the staging machine, to which the data should be uploaded. The passwords to both accounts are the same. The "data staging machine" is a temporary data storage, which is inside the AMC and can be accessed (only from the AMC network) via a ftp client program like winscp, fireftp. For the examples on these user documentations we are using fireftp.

e-BioinfraGate User Documentation

Registration

e-BioinfraGate User Documentation

Using DTI Atlas

e-BioinfraGate User Documentation

e-BioinfraGate User Documentation

Using DTI Atlas

Registration

In order to use the e-BioinfraGate, users should register like the following:

1. Our administration will inform you via email as soon as your account is activated.

Your account includes access privileges to the e-BioinfraGate website and to the staging machine, to which the data should be uploaded. The passwords to both accounts are the same. The staging machine is a temporary data storage, which is inside the AMC and can be accessed (only from the AMC network) via a ftp client program like winscp, fireftp. For the examples on this manual we are using fireftp.

Using Freesurfer

Submission of an experement

Retrieval of the results of an experiment

e-BioinfraGate User Documentation

Using DTI Atlas

e-BioinfraGate User Documentation

Retrieval of the results of an experiment

e-BioinfraGate User Documentation

Using Freesurfer

Submission of an experement

Retrieval of the results of an experiment

e-BioinfraGate User Documentation

The e-BioinfraGate is a web application and can be found here

Registration

Retrieval of the results of an experiment

e-BioinfraGate User Documentation

Registration

In order to use the e-BioinfraGate, users should register like the following:

1. Contact the administration via email or via phone (+31-20-5664717) in order to activate your account.
2. Our administration will inform you via email as soon as your account is activated.

Using Freesurfer

Submission of an experement

Retrieval of the results of an experiment

Using DTI Atlas