1-5 October 2007
Europe Congress Center
Europe/Zurich timezone

Enabling Distributed Processing of Bioinformatics Data in Hellas Grid Environment

Not scheduled
1m
Europe Congress Center

Europe Congress Center

Budapest Hungary
Poster Demo and Poster session

Speaker

Prof. Ilias Maglogiannis (University of Aegean)

Report on the experience (or the proposed activity). It would be very important to mention key services which are essential for the success of your activity on the EGEE infrastructure.

The developed microarray processing algorithms have been initially provided by as a set of MATLAB libraries. However, no nodes of the Hellenic Grid Infrastructure provide support for MATLAB execution. Furthermore MATLAB is a commercial product, which raises intricate licensing issues when it comes to installing it in the Grid and makes it unlikely to become available in the near future. Therefore, we have investigated possible alternatives, the most prominent being the use of Octave Forge, which is the GNU open-source alternative to MATLAB. Accordingly, we dealt with the task of parallelizing the (Octave Forge) microarray application and making it appropriate for use over the Grid. During grid programming we introduced a hierarchical system of sub-jobs. It is likely that a job could utilize the services of the grid environment to launch one or more sub-jobs.

Describe the scientific/technical community and the scientific/technical activity using (planning to use) the EGEE infrastructure. A high-level description is needed (neither a detailed specialist report nor a list of references).

In this work we present a Web based portal, which enables intelligent processing of biological data in Grid environments. The deployed software aims at creation of tools for processing data from microarray experiments over the Hellenic Grid infrastructure. This work serves as a starting point for building a more complete and integrated Grid enabled microarray experimentation environment.

Describe the added value of the Grid for the scientific/technical activity you (plan to) do on the Grid. This should include the scale of the activity and of the potential user community and the relevance for other scientific or business applications

Users accessing the Web Interface through the implemented portal are given the ability to submit their experiments, retrieve their results and also compare them with formerly submitted experiments. Since the portal is set up on Hellas Grid User Interface (HG-UI), users have the ability to actually access the whole Grid infrastructure, consisting of many grid nodes. Access to services is enabled by parsing input files and accordingly activating the ‘gridified’ algorithms for processing the microarray experiments. Both data parsing operations and launching of experiments are specified as Grid jobs, using the Job Description Language (JDL). The provided microarray input files, which are usually structured according to formats that are standard for the microarray bioinformatics community are pre-processed so as so to be usable by the range of algorithms available.

Primary author

Prof. Ilias Maglogiannis (University of Aegean)

Co-authors

Dr Aris Chatzioannou (NHRF) Mr Ioannis Kanaris (University of Aegean) Prof. Ioannis Soldatos (AIT) Mr Vassilis Mylonakis (University of Aegean)

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