Difference: EBioinfraGateUserDoc (1 vs. 41)

Revision 412013-05-06 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 38 to 38
  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.
Added:
>
>
  • 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.

Revision 402013-02-12 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Added:
>
>
 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:

Revision 392012-10-09 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 52 to 52
 

Publications

Changed:
<
<
  • S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, Accepted.
  • 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. 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
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1344268472" name="registration-form.PNG" path="registration-form.PNG" size="65511" user="ShayanShahand" version="3"

Revision 382012-08-06 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 9 to 9
 
Changed:
<
<
The e-BioinfraGateway 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) and the AMC ICT Innovation Fund (research).
>
>
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

Added:
>
>
 

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
Line: 57 to 52
 

Publications

Added:
>
>
  • S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, Accepted.
 
  • 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
Deleted:
<
<
  • S. Shahand, M. Santcroos, A. H. van Kampen, and S. Olabarriaga. A Grid-enabled Gateway for Biomedical Data Analysis. Submitted.
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
Changed:
<
<
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"
>
>
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1344268472" name="registration-form.PNG" path="registration-form.PNG" size="65511" user="ShayanShahand" version="3"
 
META FILEATTACHMENT attachment="ebioinfragate.pdf" attr="" comment="healthgrid 2011 paper" date="1312204956" name="ebioinfragate.pdf" path="ebioinfragate.pdf" size="250223" user="ShayanShahand" version="1"
META TOPICMOVED by="ShayanShahand" date="1293722968" from="EBioScience/EBioInternal.EbioinfragateUserDoc" to="EBioScience.EBioinfraGateUserDoc"

Revision 372012-04-06 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 10 to 10
 
Added:
>
>
 
    • DTI Atlas: registration of large collections of DTI images
    • Freesurfer: brain surface segmentation
    • BLAST: alignment of DNA sequence data with a given database
Changed:
<
<
>
>
 The e-BioinfraGateway 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) and the AMC ICT Innovation Fund (research).

For more information please contact us.

Revision 362012-03-16 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 41 to 41
 
  • 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.)
Changed:
<
<
  • 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 SFTP protocol that is used for securely transport your files.
>
>
  • 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

Revision 352012-03-16 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 7 to 7
  The following steps are needed to use the e-BioinfraGateway:
Changed:
<
<
>
>
 
Line: 22 to 22
 

Changed:
<
<

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
>
>

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

Line: 35 to 35
  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.
Changed:
<
<
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).
>
>
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.
  • 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.)
Added:
>
>
  • 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 SFTP protocol that is used for securely transport your files.
 

Applications

Revision 342012-01-31 - KyriacosNeocleous

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 50 to 50
 
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
Changed:
<
<
Genome Compare   Genome Compare User Documentation
>
>
Genome Compare counts and clusters homologous genes to find related strains Genome Compare User Documentation
 
Changed:
<
<

Publication

>
>

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

Revision 332011-12-21 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 54 to 54
 

Publication

Changed:
<
<
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Proceedings of the HealthGrid 2011, 2011. PDF
>
>
  • 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.
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 322011-10-18 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 38 to 38
 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).

Important Notes:

Added:
>
>
  • 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.)

Revision 312011-10-07 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 53 to 53
 

Publication

Changed:
<
<
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference .PDF
>
>
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Proceedings of the HealthGrid 2011, 2011. PDF
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 302011-08-23 - SouleyMadougou

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 33 to 33
 

Data Transport

Changed:
<
<
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.
>
>
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 this version of FileZilla, which does not require installation (i.e., unzip and use).
Line: 49 to 49
 
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
Changed:
<
<
Genome Compare    
>
>
Genome Compare   Genome Compare User Documentation
 

Publication

Revision 292011-08-22 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 30 to 30
  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.
Added:
>
>
 

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).

Added:
>
>
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.)
 

Applications

Application Name Function Documentation

Revision 282011-08-19 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Changed:
<
<
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/
>
>
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://www.ebioscience.amc.nl/ebioinfragateway/
  The following steps are needed to use the e-BioinfraGateway:
Line: 22 to 22
 

Changed:
<
<

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
>
>

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

Revision 272011-08-01 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 47 to 47
 

Publication

Changed:
<
<
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference.
>
>
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference .PDF
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"
Added:
>
>
META FILEATTACHMENT attachment="ebioinfragate.pdf" attr="" comment="healthgrid 2011 paper" date="1312204956" name="ebioinfragate.pdf" path="ebioinfragate.pdf" size="250223" user="ShayanShahand" version="1"
 
META TOPICMOVED by="ShayanShahand" date="1293722968" from="EBioScience/EBioInternal.EbioinfragateUserDoc" to="EBioScience.EBioinfraGateUserDoc"

Revision 262011-07-05 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 14 to 14
 
Changed:
<
<
The e-BioinfraGateway 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) and the AMC ICT Innovation Fund (research).
>
>
The e-BioinfraGateway 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) and the AMC ICT Innovation Fund (research).
  For more information please contact us.
Line: 24 to 24
 

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
Added:
>
>

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 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.

Line: 41 to 47
 

Publication

Changed:
<
<
S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference.
>
>
  • S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference.
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 252011-05-25 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 22 to 22
 

Changed:
<
<

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. 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
>
>

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
 

Data Transport

Line: 37 to 37
 
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
Added:
>
>
Genome Compare    

Publication

S. Shahand, M. Santcroos, Y. Mohammed, V. Korkhov, A. C. M. Luyf, A. van Kampen, S. Olabarriaga, "Front-ends to Biomedical Data Analysis on Grids", Submitted to the HealthGrid 2011 conference.

 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 242011-05-03 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Changed:
<
<
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/
>
>
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/
 
Changed:
<
<
The following steps are needed to use the e-bioinfragateway:
>
>
The following steps are needed to use the e-BioinfraGateway:
 
Line: 13 to 13
 
    • DTI Atlas: registration of large collections of DTI images
    • Freesurfer: brain surface segmentation
    • BLAST: alignment of DNA sequence data with a given database
Changed:
<
<
The e-bioinfragateway 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) and the AMC ICT Innovation Fund (research).
>
>
The e-BioinfraGateway 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) and the AMC ICT Innovation Fund (research).
  For more information please contact us.
Line: 31 to 32
 

Applications

Application Name Function Documentation
Changed:
<
<
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
>
>
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
 
META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 232011-04-28 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

Medical Bioinformatics and e-Bioscience

e-BioinfraGateway

Line: 27 to 27
  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.
Changed:
<
<
Files can be copied to/from this space by the researcher using regular ftp client programs such as winscp and fireftp. For the examples on the user documentation we are using fireftp.
>
>
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

Application Name Function Documentation

Revision 222011-04-21 - AngelaLuijf

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"
Added:
>
>

Medical Bioinformatics and e-Bioscience

 

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/

Revision 212011-04-19 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGateway

Line: 8 to 8
 
Added:
>
>
 
    • DTI Atlas: registration of large collections of DTI images
    • Freesurfer: brain surface segmentation
    • BLAST: alignment of DNA sequence data with a given database

Revision 202011-03-07 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGateway

Revision 192011-02-22 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"
Changed:
<
<

e-BioinfraGate

>
>

e-BioinfraGateway

 
Changed:
<
<
The e-Bioinfra Gateway (e-bioinfragate) 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/ebioinfragate/
>
>
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/
 
Changed:
<
<
The following steps are needed to use the e-bioinfragate:
>
>
The following steps are needed to use the e-bioinfragateway:
 
Changed:
<
<
The e-bioinfragate 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) and the AMC ICT Innovation Fund (research).
>
>
    • BLAST: alignment of DNA sequence data with a given database
The e-bioinfragateway 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) and the AMC ICT Innovation Fund (research).
  For more information please contact us.
Line: 18 to 19
 

Changed:
<
<

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and conditions.
  2. Our administration will inform you via email as soon as your account is activated.

NOTE:

Your account includes access privileges to the e-BioinfraGate 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
>
>

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. 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
 

Data Transport

Line: 28 to 29
 

Applications

Application Name Function Documentation
Changed:
<
<
DTI Atlas registration of large collections of DTI images DTI Atlas on the e-bioinfragate User Documentation
Freesurfer brain surface segmentation from MRI images Freesurfer on the e-bioinfragate 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
 
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META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"

Revision 182011-01-18 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate

Changed:
<
<
The e-Bioinfra Gateway (e-bioinfragate) 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/ebioinfragate/
>
>
The e-Bioinfra Gateway (e-bioinfragate) 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/ebioinfragate/
  The following steps are needed to use the e-bioinfragate:
Line: 31 to 31
 
DTI Atlas registration of large collections of DTI images DTI Atlas on the e-bioinfragate User Documentation
Freesurfer brain surface segmentation from MRI images Freesurfer on the e-bioinfragate User Documentation
Deleted:
<
<
META FILEATTACHMENT attachment="1_welcome.png" attr="h" comment="" date="1293713758" name="1_welcome.png" path="1_welcome.png" size="94090" stream="1_welcome.png" tmpFilename="/var/tmp/CGItemp25778" user="YasseneMohammed" version="1"
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META FILEATTACHMENT attachment="ebioinfragate.PNG" attr="h" comment="" date="1295019201" name="ebioinfragate.PNG" path="ebioinfragate.PNG" size="283208" user="ShayanShahand" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="myexperiments.PNG" attr="h" comment="" date="1295019198" name="myexperiments.PNG" path="myexperiments.PNG" size="176029" user="ShayanShahand" version="1"
META FILEATTACHMENT attachment="experiment-information.PNG" attr="h" comment="" date="1295019197" name="experiment-information.PNG" path="experiment-information.PNG" size="112521" user="ShayanShahand" version="1"
 
META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="1.png" attr="h" comment="" date="1295263211" name="1.png" path="1.png" size="204927" user="YasseneMohammed" version="1"
 
META TOPICMOVED by="ShayanShahand" date="1293722968" from="EBioScience/EBioInternal.EbioinfragateUserDoc" to="EBioScience.EBioinfraGateUserDoc"

Revision 172011-01-18 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate

Line: 28 to 28
 

Applications

Application Name Function Documentation
Changed:
<
<
DTI Atlas registration of large collections of DTI images DTIAtlasUserDoc
Freesurfer brain surface segmentation from MRI images FreesurferUserDoc
>
>
DTI Atlas registration of large collections of DTI images DTI Atlas on the e-bioinfragate User Documentation
Freesurfer brain surface segmentation from MRI images Freesurfer on the e-bioinfragate User Documentation
 
META FILEATTACHMENT attachment="1_welcome.png" attr="h" comment="" date="1293713758" name="1_welcome.png" path="1_welcome.png" size="94090" stream="1_welcome.png" tmpFilename="/var/tmp/CGItemp25778" user="YasseneMohammed" version="1"
META FILEATTACHMENT attachment="2.png" attr="h" comment="" date="1293713768" name="2.png" path="2.png" size="58972" stream="2.png" tmpFilename="/var/tmp/CGItemp25887" user="YasseneMohammed" version="1"

Revision 162011-01-17 - SilviaOlabarriaga

Line: 1 to 1
 
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate

Changed:
<
<
The e-Bioinfra Gateway (e-bioinfragate) is a web application developed by the e-BioScience team of the Bioinformatics Laboratory of the AMC, Department of Epidemiology, Biostatistics and Bioinformatics (KEBB). It 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 e-Bioinfra Gateway (e-bioinfragate) 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/ebioinfragate/
 
Changed:
<
<
The web link and can be found at http://orange.ebioscience.amc.nl/ebioinfragate/

To use it the following steps are needed:

>
>
The following steps are needed to use the e-bioinfragate:
 
    • DTI Atlas: registration of large collections of DTI images
    • Freesurfer: brain surface segmentation
Changed:
<
<
For more information please [[][contact us]]
>
>
The e-bioinfragate 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) and the AMC ICT Innovation Fund (research).

For more information please contact us.

 

Registration

Changed:
<
<

>
>

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and conditions.
  2. Our administration will inform you via email as soon as your account is activated.

NOTE:

Your account includes access privileges to the e-BioinfraGate 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

Data Transport

 
Changed:
<
<

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and condition.
  2. 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.
registration-form.PNG
>
>
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.
 
Added:
>
>
Files can be copied to/from this space by the researcher using regular ftp client programs such as winscp and fireftp. For the examples on the user documentation we are using fireftp.
 

Applications

Changed:
<
<
Application Name Application Specific User Documentation
DTI Atlas DTIAtlasUserDoc
Freesurfer FreesurferUserDoc
>
>
Application Name Function Documentation
DTI Atlas registration of large collections of DTI images DTIAtlasUserDoc
Freesurfer brain surface segmentation from MRI images FreesurferUserDoc
 
META FILEATTACHMENT attachment="1_welcome.png" attr="h" comment="" date="1293713758" name="1_welcome.png" path="1_welcome.png" size="94090" stream="1_welcome.png" tmpFilename="/var/tmp/CGItemp25778" user="YasseneMohammed" version="1"
META FILEATTACHMENT attachment="2.png" attr="h" comment="" date="1293713768" name="2.png" path="2.png" size="58972" stream="2.png" tmpFilename="/var/tmp/CGItemp25887" user="YasseneMohammed" version="1"

Revision 152011-01-17 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate

Line: 14 to 14
 For more information please [[][contact us]]

Registration

Changed:
<
<

>
>

 

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and condition.
  2. 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.
registration-form.PNG

Revision 142011-01-17 - SilviaOlabarriaga

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"
Changed:
<
<

e-BioinfraGate User Documentation

>
>

e-BioinfraGate

 
Changed:
<
<
The e-Bioinfra Gateway (e-bioinfragate) is a web application and can be found at http://orange.ebioscience.amc.nl/ebioinfragate/
>
>
The e-Bioinfra Gateway (e-bioinfragate) is a web application developed by the e-BioScience team of the Bioinformatics Laboratory of the AMC, Department of Epidemiology, Biostatistics and Bioinformatics (KEBB). It 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.
 
Changed:
<
<
>
>
The web link and can be found at http://orange.ebioscience.amc.nl/ebioinfragate/
 
Added:
>
>
To use it the following steps are needed: For more information please [[][contact us]]
 

Registration

Revision 132011-01-17 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate User Documentation

Line: 10 to 10
 

Registration

Added:
>
>

 

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and condition.
  2. 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.
registration-form.PNG

Applications

Revision 122011-01-17 - YasseneMohammed

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

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/

Changed:
<
<
>
>
 

Registration

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and condition.
  2. 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.
registration-form.PNG
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Added:
>
>
META FILEATTACHMENT attachment="1.png" attr="h" comment="" date="1295263211" name="1.png" path="1.png" size="204927" user="YasseneMohammed" version="1"
 
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Revision 112011-01-17 - ShayanShahand

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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate User Documentation

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

Registration

Added:
>
>

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

  1. 1 Provide the needed information on the registration web page, and agree to the terms and condition.
  2. 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.
registration-form.PNG

Applications

 
Changed:
<
<
In order to use the e-BioinfraGate, users should register like the following:
  1. Provide the needed information on the registration web page, choose the applications you intend to use by requesting the corresponding roles, and agree to the terms and condition.
  2. Contact the administration via email or via phone (+31-20-5664717) in order to activate your account.
  3. 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.

Uploading Input Data

Using Freesurfer

Submission of an experement

1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
5. Upload your data to the staging machine under the path which looks like "/project/gridsync/username/inputs/freesurfer/". After that it will take around 30 minutes for the data staging machine to push the data to the Grid, i.e. the data will be ready for processing.  
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names are partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
11. Press on Start Experiment to start processing your data on the Grid.  

Retrieval of the results of an experiment

1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
2. Choose Profile from the Toolbox menu on the left.  
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
4. By clicking on the Experiment ID you can obtain a list of information about your experiment.  
5. By clicking on the Workflow ID you can obtain advanced information about the workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  

Using DTI Atlas

1. Login to the e-BioinfraGate website with your username and password, and click on the "DTI Atlas" picture to start. ebioinfragate.PNG
2. After successful login, you will see a brief introduction about the DTI Atlas experiment. Click on "next". dti1.PNG
3. In the "upload" step you have to upload your input data to the "data staging machine". Use the link provided on this step and your favorite FTP client to upload input files from your desktop to the "data staging machine" (currently the "data staging machine" is only accessible from within the AMC network). You should use the same username and password you used for e-bioinfragate to login to the "data staging machine". When you have uploaded the input files to the "data staging machine", please come back to the ebioinfragate and click on "next" to see if your input files already arrived on the Grid. dti2.PNG
4. Select the input files you wish to perform experiments on them and click on "next". dti3.PNG
5. Provide a name for your experiment (so you can identify it later) and click on "start experiments". dti4.PNG
6. When the experiment started successfully, you see this confirmation page, please click on the link provided to go to "experiments summary" page. dti5.PNG
7. On the "experiments summary" page you can see an overview of all of your experiments. Click on the "latest status" of a particular experiment to see more details about that experiment. myexperiments.PNG
8. On the experiment information page, click on the "refresh status" button to update the experiment status. When the experiment finished successfully (i.e., the status is finished) you can see the link to the results on the data staging machine where you can collect the results. If you don't see all of the results on the data staging machine, please wait for one hour to make sure all of the results have been fetched from the Grid. experiment-information.PNG
>
>
Application Name Application Specific User Documentation
DTI Atlas DTIAtlasUserDoc
Freesurfer FreesurferUserDoc
 
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<
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META FILEATTACHMENT attachment="registration-form.PNG" attr="h" comment="" date="1295257363" name="registration-form.PNG" path="registration-form.PNG" size="76096" user="ShayanShahand" version="1"
 
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META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate User Documentation

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6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  

Using DTI Atlas

Changed:
<
<
1. Login to the e-BioinfraGate website with your username and password, or click on the "DTI Atlas" picture to login ebioinfragate.PNG
2. After successful login, you will see a brief introduction about DTI Atlas experiment. Click on next dti1.PNG
3. In the upload step you have to upload your input data to the data staging machine. Use the link provided on this step and your favorite FTP client to upload input files to the "data staging" machine. After uploading the input files, please come back to the ebioinfragate and click on next to see if your input files already arrived on the Grid. dti2.PNG
4. Select the input files you wish to perform experiments on them and click on next dti3.PNG
5. Provide a name for your experiment so you can identify it later and click on start experiment dti4.PNG
6. When the experiment started successfully, you see this confirmation, please click on the link provided to go to "my experiments" page. dti5.PNG
7. On the "my experiments" page you can see an overview of all of your experiments. Click on the "experiment status" to see more details about the experiment myexperiments.PNG
8. On the experiment information page, click on the "refresh status" button to update the experiment status. Once the experiment finished successfully (i.e., the status is finished) you can see the link to the results on the data staging machine where you can collect the results. If you don't see all of the results please check the data staging machine after one hour to make sure all of the results have been fetched from the Grid. experiment-information.PNG
>
>
1. Login to the e-BioinfraGate website with your username and password, and click on the "DTI Atlas" picture to start. ebioinfragate.PNG
2. After successful login, you will see a brief introduction about the DTI Atlas experiment. Click on "next". dti1.PNG
3. In the "upload" step you have to upload your input data to the "data staging machine". Use the link provided on this step and your favorite FTP client to upload input files from your desktop to the "data staging machine" (currently the "data staging machine" is only accessible from within the AMC network). You should use the same username and password you used for e-bioinfragate to login to the "data staging machine". When you have uploaded the input files to the "data staging machine", please come back to the ebioinfragate and click on "next" to see if your input files already arrived on the Grid. dti2.PNG
4. Select the input files you wish to perform experiments on them and click on "next". dti3.PNG
5. Provide a name for your experiment (so you can identify it later) and click on "start experiments". dti4.PNG
6. When the experiment started successfully, you see this confirmation page, please click on the link provided to go to "experiments summary" page. dti5.PNG
7. On the "experiments summary" page you can see an overview of all of your experiments. Click on the "latest status" of a particular experiment to see more details about that experiment. myexperiments.PNG
8. On the experiment information page, click on the "refresh status" button to update the experiment status. When the experiment finished successfully (i.e., the status is finished) you can see the link to the results on the data staging machine where you can collect the results. If you don't see all of the results on the data staging machine, please wait for one hour to make sure all of the results have been fetched from the Grid. experiment-information.PNG
 
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>
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e-BioinfraGate User Documentation

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e-BioinfraGate User Documentation

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6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  

Using DTI Atlas

Changed:
<
<

Submission of an experiment

Retrieval of the results of an experiment

>
>
1. Login to the e-BioinfraGate website with your username and password, or click on the "DTI Atlas" picture to login ebioinfragate.PNG
2. After successful login, you will see a brief introduction about DTI Atlas experiment. Click on next dti1.PNG
3. In the upload step you have to upload your input data to the data staging machine. Use the link provided on this step and your favorite FTP client to upload input files to the "data staging" machine. After uploading the input files, please come back to the ebioinfragate and click on next to see if your input files already arrived on the Grid. dti2.PNG
4. Select the input files you wish to perform experiments on them and click on next dti3.PNG
5. Provide a name for your experiment so you can identify it later and click on start experiment dti4.PNG
6. When the experiment started successfully, you see this confirmation, please click on the link provided to go to "my experiments" page. dti5.PNG
7. On the "my experiments" page you can see an overview of all of your experiments. Click on the "experiment status" to see more details about the experiment myexperiments.PNG
8. On the experiment information page, click on the "refresh status" button to update the experiment status. Once the experiment finished successfully (i.e., the status is finished) you can see the link to the results on the data staging machine where you can collect the results. If you don't see all of the results please check the data staging machine after one hour to make sure all of the results have been fetched from the Grid. experiment-information.PNG
 
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META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

>
>
META TOPICPARENT name="EBioScience/EBioInternal.NewEBioinfraArchitecture"

e-BioinfraGate User Documentation

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

>
>
 

Registration

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

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  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.

Added:
>
>

Uploading Input Data

 

Using Freesurfer

Submission of an experement

Changed:
<
<
1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
>
>
1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
 
5. Upload your data to the staging machine under the path which looks like "/project/gridsync/username/inputs/freesurfer/". After that it will take around 30 minutes for the data staging machine to push the data to the Grid, i.e. the data will be ready for processing.  
Changed:
<
<
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
>
>
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
 
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
Changed:
<
<
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
>
>
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
 
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names are partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
11. Press on Start Experiment to start processing your data on the Grid.  

Retrieval of the results of an experiment

Changed:
<
<
1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
>
>
1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
 
2. Choose Profile from the Toolbox menu on the left.  
Changed:
<
<
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
>
>
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
 
4. By clicking on the Experiment ID you can obtain a list of information about your experiment.  
5. By clicking on the Workflow ID you can obtain advanced information about the workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  
Changed:
<
<

Using DTI Atlas

>
>

Using DTI Atlas

Submission of an experiment

Retrieval of the results of an experiment

 
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META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

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6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  

Using DTI Atlas

Changed:
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<
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>
>
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Revision 52010-12-30 - YasseneMohammed

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META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

Line: 25 to 25
 
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
Changed:
<
<
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
>
>
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names are partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
 
11. Press on Start Experiment to start processing your data on the Grid.  

Retrieval of the results of an experiment

Revision 42010-12-30 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

Line: 16 to 16
 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

Changed:
<
<
1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
>
>
1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
 
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
Changed:
<
<
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
>
>
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
 
5. Upload your data to the staging machine under the path which looks like "/project/gridsync/username/inputs/freesurfer/". After that it will take around 30 minutes for the data staging machine to push the data to the Grid, i.e. the data will be ready for processing.  
Changed:
<
<
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
>
>
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
 
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
Changed:
<
<
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
>
>
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
 
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
11. Press on Start Experiment to start processing your data on the Grid.  

Retrieval of the results of an experiment

Changed:
<
<
1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
>
>
1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
 
2. Choose Profile from the Toolbox menu on the left.  
Changed:
<
<
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
>
>
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
 
4. By clicking on the Experiment ID you can obtain a list of information about your experiment.  
5. By clicking on the Workflow ID you can obtain advanced information about the workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  

Revision 32010-12-30 - YasseneMohammed

Line: 1 to 1
 
META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

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

Added:
>
>
 

Registration

Line: 24 to 25
 
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
Changed:
<
<
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill".  
>
>
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill". If the names partially identical, you can still use this option and then do minimal changes, e.g. change only the path (T0 to T1 in our example here).  
 
11. Press on Start Experiment to start processing your data on the Grid.  

Retrieval of the results of an experiment

Revision 22010-12-30 - ShayanShahand

Line: 1 to 1
 
META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

Line: 8 to 8
 

Registration

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

Changed:
<
<
  1. Provide the needed information on the registration website, choose the applications you intend by requesting the corresponding roles, and agree to the terms and condition.
>
>
  1. Provide the needed information on the registration web page, choose the applications you intend to use by requesting the corresponding roles, and agree to the terms and condition.
 
  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.
Changed:
<
<
Your account includes access privileges to the e-BioinfraGate website and to the staging machine, to which the data should be uploaded. The password to both accounts is the same. The staging machine is a temporary data storage, which is inside the AMC and can be accessed via an ftp client program like winscp, fireftp). For the examples on this site we are using fireftp.
>
>
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

Changed:
<
<
1. Login on the e-BioinfraGate using your user name and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload website opens. 3.png
4. Use your favorite ftp client to upload the data to the staging machine. If you are using fireftp, just click on the link provided on the page. If you using another client, connect to 145.117.12.67 with your user name and password, which are the same as for the e-BioinfraGate website. 4.png
5. Upload your data to the staging machine. After that it will take around 15 min for the staging machine to push the data to the grid, i.e. the data will be ready for processing  
6. Go to the Upload site, either by clicking "back" in your browser if you are using fireftp or by logging again if you are already logged out. 3.png
7. Click on Next. The Input Selection website opens and here you should see a list of all the data you moved to the staging machine. 5.png
8. Choose the data you want to process, either by clicking on Select All button or by choosing the datasets individually.  
9. Click on Next. The Experiment Configuration website will open. Here you should fill all the needed configurations for your experiment. 6.png
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on Auto Fill. If the names partially  
11. Press on Start Experiment to start processing your data.  
>
>
1. Login on the e-BioinfraGate using your username and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload page containing the instructions about how to upload input files opens. Use the link provided on this page to upload your input files to the data staging machine. 3.png
4. Use your favorite ftp client to upload the data to the data staging machine. If you are using fireftp, just click on the link provided on the page. If you are using another client, connect to 145.117.12.67 with your username and password, which are the same as for the e-BioinfraGate website. 4.png
5. Upload your data to the staging machine under the path which looks like "/project/gridsync/username/inputs/freesurfer/". After that it will take around 30 minutes for the data staging machine to push the data to the Grid, i.e. the data will be ready for processing.  
6. Go back to the e-BioinfraGate site (e.g., by clicking "back" in your browser if you are using fireftp) where you left off (i.e., upload page). 3.png
7. Click on Next to see if your input files have already been arrived on the Grid. The Input Selection website opens and here you should see a list of all of your input data. 5.png
8. Choose the data you want to process. Click on "Select All" button if you wish to select all of the input files. You can also choose a number of input files by holding "ctrl" or "cmd" key.  
9. Click on Next. The Experiment Configuration page will open. Here you should fill all the needed configurations for your experiment. 6.png
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on "Auto Fill".  
11. Press on Start Experiment to start processing your data on the Grid.  
 

Retrieval of the results of an experiment

Changed:
<
<
1. Login to the e-BioinfraGate website with your user name and password 1_welcome.png
>
>
1. Login to the e-BioinfraGate website with your username and password 1_welcome.png
 
2. Choose Profile from the Toolbox menu on the left.  
Changed:
<
<
3. The Scientist Information website open. Here you should be able to see all experiments you submitted. 7.png
4. By clicking on the Experiment ID you can obtain a list of information about your experiment  
5. By clicking on the Workflow ID you can obtain advanced information about the running/run workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result.  
>
>
3. The Scientist Information website opens. Here you should be able to see all of the experiments you submitted. 7.png
4. By clicking on the Experiment ID you can obtain a list of information about your experiment.  
5. By clicking on the Workflow ID you can obtain advanced information about the workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result on the data staging machine.  
 

Using DTI Atlas

META FILEATTACHMENT attachment="1_welcome.png" attr="" comment="" date="1293713758" name="1_welcome.png" path="1_welcome.png" size="94090" stream="1_welcome.png" tmpFilename="/var/tmp/CGItemp25778" user="YasseneMohammed" version="1"

Revision 12010-12-30 - YasseneMohammed

Line: 1 to 1
Added:
>
>
META TOPICPARENT name="Ebioinfragate"

e-BioinfraGate User Documentation

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

Registration

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

  1. Provide the needed information on the registration website, choose the applications you intend by requesting the corresponding roles, and agree to the terms and condition.
  2. Contact the administration via email or via phone (+31-20-5664717) in order to activate your account.
  3. 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 password to both accounts is the same. The staging machine is a temporary data storage, which is inside the AMC and can be accessed via an ftp client program like winscp, fireftp). For the examples on this site we are using fireftp.

Using Freesurfer

Submission of an experement

1. Login on the e-BioinfraGate using your user name and password. The welcome website opens. 1_welcome.png
2. Choose Freesurfer from the Toolbox menu on the left. 2.png
3. Click next. The Upload website opens. 3.png
4. Use your favorite ftp client to upload the data to the staging machine. If you are using fireftp, just click on the link provided on the page. If you using another client, connect to 145.117.12.67 with your user name and password, which are the same as for the e-BioinfraGate website. 4.png
5. Upload your data to the staging machine. After that it will take around 15 min for the staging machine to push the data to the grid, i.e. the data will be ready for processing  
6. Go to the Upload site, either by clicking "back" in your browser if you are using fireftp or by logging again if you are already logged out. 3.png
7. Click on Next. The Input Selection website opens and here you should see a list of all the data you moved to the staging machine. 5.png
8. Choose the data you want to process, either by clicking on Select All button or by choosing the datasets individually.  
9. Click on Next. The Experiment Configuration website will open. Here you should fill all the needed configurations for your experiment. 6.png
10. If the names of the "first file in series" of all input datasets are identical, you can write the first one and then press on Auto Fill. If the names partially  
11. Press on Start Experiment to start processing your data.  

Retrieval of the results of an experiment

1. Login to the e-BioinfraGate website with your user name and password 1_welcome.png
2. Choose Profile from the Toolbox menu on the left.  
3. The Scientist Information website open. Here you should be able to see all experiments you submitted. 7.png
4. By clicking on the Experiment ID you can obtain a list of information about your experiment  
5. By clicking on the Workflow ID you can obtain advanced information about the running/run workflow (this option is for advanced user, e.g. for debugging, seeing std.out, std.err, workflow.out, etc.)  
6. By clicking on the Result Location (and if you are using fireftp as an FTP client) a FTP client window will open, which point directly to the experiment result.  

Using DTI Atlas

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