Medical Bioinformatics and e-Bioscience

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Getting Started on the e-BioInfra

NOTE: we recommend to follow the complete guide from one single computer using the default configurations. This will make prevent problems due to missing files or inconsistent configurations.

Normally files will be stored on your "HOME" directory:

• On Windows this is somewhere under ........\profiles\<your name>. To know it for sure, do the following

start a cmd window
find out the name of the current directory. This is your home

• On linux this will be given by $HOME

Obtain a grid certificate

A grid certificate is a "passport" for using grid resources that is emmitted by the DutchGrid certificate authority. To obtain one go to

• https://ca.dutchgrid.nl/start/: this is the new friendly (web-based) procedure. It installs a program automatically in your computer that looks around and puts the right files on the right place. Just read carefully the instructions on the screen and follow them. Note: This needs to be executed from your own workstation because it will write files in it (and you need to keep these files)
• http://www.dutchgrid.nl/ca/request/: this is the more general site for "die hards"; it will require more expertise. Follow the instructions carefully.

When asked (on the web form) please inform the following:

• Certificate of type: "Users (personal certificates)"
• Your Organisation: uva, Unit: amc (or other applicable)
• Certification level: "Medium security"

After your request has been processed (in both cases above), you'll receive an e-mail from the CA (certification authority) with further instructions. Note that this may take a few days. If you are using the new user-friendly web interface, most of the steps are done automatically for you.

At the end of the process JGridStart will ask you to "load your certificate into the browser", which needs to be done to enable you to visit various grid-relared websites without typing any additional password.

More detailed info:

• General info on SARA's wiki
• See here how to manually load your certificate into the web browser

For the impatient: While you are waiting for your grid certificate, you can check on the common practices in creating workflows.

Become a member of a Virtual Organization (VO)

"Virtual Organizations" are collections of persons that share grid resources. There are various VOs in the Dutch Grid (see existing communities), each of them offers different support and services. The e-!BioInfra currently only supports the VLEMED VO.

Go here to become a "member" of VLEMED. Note: before doing this, you need to "load your certificate into the web browser in your workstation". This is the last step done automatically by JGridStart.

Your request will be approved by the "VO manager" and after that you will be able to use the grid.

More detailed info:

• General info on SARA's wiki
• See here how to load your certificate into the web browser

Download and install the VBrowser

The VBrowser is a program that needs to be installed in your own workstation to facilitate access to the grid.

For more information about the VBrowser, how to download and configure, please refer to the VBrowser page.

Subscribe to the user's mailing list

A mailing list is used for announcements about all types of relevant events, from interruption or maintenance of grid services, modifications in the configuration, etc.

Please send a mail to ebioscience-support@amc.uva.nl and request to be added to the mailing list.

Run your first job

Check SARA's wiki page:

https://grid.sara.nl/wiki/index.php/Using_the_Grid/#Job_submission:_Basic

Run your first workflow

Where to go from here

• From executable to workflow
• MOTEUR