BioPortal benefits from excellent support

By Simon Hettrick

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The Irish BioPortal Project, managed by the Irish Centre for High End Computing (ICHEC), will establish a central web portal where researchers can interface with bioinformatics applications, submit jobs to back-end compute systems and obtain their results – all in an efficient, timely and user-friendly fashion. ICHEC recently praised OMII-UK for its ‘excellent and timely support’ in providing them with the bespoke functionality they needed for their project’s job submission service.

In June 2009, Kashif Iqbal, a software developer at ICHEC, contacted OMII-UK with a problem. He had chosen to use GridSAM for job submission, because it can interface with a number of different back-end compute systems (PBS, Torque, Condor, etc.), and allowed job submission to multiple resource managers using SSH. However, the then-current GridSAM provided control using a single SSH account, whereas the Irish Bioportal project needed a separate account for each user.

Implementing the functionality required by ICHEC necessitated significant changes to the GridSAM code. An Axis/SOAP infrastructure was added so that user credentials used by the back-end job-submission system could be articulated from the GridSAM client, a GridSAM infrastructure was added to allow user credentials to read and persisted within the job details, and the way GridSAM communicated with the back-end systems was altered so that it could pass credentials for use with SSH. It would be typical to expect many months to elapse before changes of this magnitude could be designed, coded and tested. OMII-UK’s developers, Justin Bradley and Steve Crouch, pushed out a new version of GridSAM with all of the changes needed by ICHEC in only four months.

ICHEC aim to have a version of the BioPortal available for testing by Autumn 2010, followed by the release of the first, publicly accessible version in mid-2011.

www.ichec.ie