An Application Platform Enabling High Performance Grid Processing of Microarray Experiments

Chatzioannou, A.; Soldatos, John; Mylonakis, Vasileios; Kanaris, Y.

doi:10.1109/cbms.2007.19

Cited by 5 publications

(2 citation statements)

References 6 publications

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“…A microarray experiment can be defined as a set of one or more hybridisations, each of which relates one or more samples to one or more arrays. The complete analysis of microarray gene expression data consists of many steps, starting with image processing, annotation, data normalization and transformation, gene sub-selection and filtering [14]. The analysis that follows can be one of many available techniques, e.g.…”

Section: Overview Of the Hector Microarray Applicationmentioning

confidence: 99%

HECTOR: Enabling Microarray Experiments over the Hellenic Grid Infrastructure

et al. 2009

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Biologists, medical experts, biochemical engineers and researchers working on DNA microarray experiments are increasingly turning on Grid computing with the scope of leveraging the Grid's computing power, immense storage resources, and quality of service to the expedient processing of a wide range of datasets. In this paper we present a combined experience of grid application experts and bioinformatics scientists in deploying a pilot service enabling computationally efficient processing and analysis of data stemming from microarray experiments. This pilot service is accessible over the Hellenic portion of the EGEE grid and has been demonstrated in the scope of several public events. We highlight the process of grid application enablement, grid deployment challenges, as well as lessons learnt from a bi-annual effort to port and deploy a MATLAB DNA microarray application on a production grid. In addition to describing the parallelization of the application, we also emphasize on the development of a distributed federated database for storing and post-processing the results of the microarray experiments. Overall we believe that our experience could be proven valuable not only to microarray data scientists but also to other Grid users that intend to Grid-enable and deploy their applications.

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Section: Overview Of the Hector Microarray Applicationmentioning

confidence: 99%

HECTOR: Enabling Microarray Experiments over the Hellenic Grid Infrastructure

et al. 2009

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“…However, the analysis algorithms are not parallelized for maximum performance and all analysis and annotation steps are single threaded executions. A seminal effort in utilizing Grid computing for DNA microarray analysis was the HECTOR platform [5], targeting cDNA chips and exploiting the Hellenic Grid infrastructure of EGEE through use of MPI technology. The implementation of Ivan Porro et al [6], is another example of such a solution, deployed over the Italian EGEE infrastructure.…”

Section: Related Workmentioning

confidence: 99%

GRISSOM web based grid portal: Exploiting the power of grid infrastructure for the interpretation and storage of DNA microarray experiments

Chatziioannou

Moulos

Pilalis

et al. 2009

2009 9th International Conference on Information Technology and Applications in Biomedicine

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DNA Microarrays have dramatically reshaped modern biological research by deriving profiles of genome-wide expression of living organisms, and producing an unprecedented wealth of quantitative data. Given this characteristic, microarray experiments are considered highthroughput both in terms of data (data intensive) and processing (computationally intensive). GRISSOM enables exploitation of GRID resources for DNA microarray distributed processing. It provides experts with a complete web-based solution for managing, searching and disseminating biological knowledge in the context of gene expression patterns on a genomic scale. The platform is developed and deployed using open source software components. Through the use of web service technologies (WSDL language) GRISSOM can be encapsulated in other biomedical processing workflows, thus rendering access to its algorithms, transparent and generic.

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A Web Based System Enabling Distributed Access and Intelligent Processing of Bioinformatics Data in Grid Environments

Soldatos

Chatzioannou

Milonakis

et al.

IFIP the International Federation for Information Processing

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This paper presents 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. Emphasis is given on user interface and access issues, while the paper describes also the data parsing and parallelization of the microarray data processing. The description of the system is oriented to Grid developers and users, since it focuses on the customization and use of the microarray applications over the Grid. Apart from supporting the high performance and economical execution of microarray experiments, the proposed system endeavors to provide access to a distributed repository of experiments information and results.

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An Application Platform Enabling High Performance Grid Processing of Microarray Experiments

Cited by 5 publications

References 6 publications

HECTOR: Enabling Microarray Experiments over the Hellenic Grid Infrastructure

HECTOR: Enabling Microarray Experiments over the Hellenic Grid Infrastructure

GRISSOM web based grid portal: Exploiting the power of grid infrastructure for the interpretation and storage of DNA microarray experiments

A Web Based System Enabling Distributed Access and Intelligent Processing of Bioinformatics Data in Grid Environments

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