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A Higher-Order Component for Efficient Genome Processing on the Grid

  • Computational grids combine computers in the Internet for distributed data processing and are an attractive platform for the data-intensive applications of bioinformatics. We present an extensible genome processing software for the grid and evaluate its performance. Our software was able to discover previously unknown circular permutations (CP) in the ProDom database containing more than 70MB of protein data. A specific feature of our software is its design as a component: the Alignment HOC, a Higher-Order Component that makes use of the latest Globus toolkit as grid middleware. Besides genome data, the Alignment HOC accepts plugin code for processing this data as its input, and contains all the required configuration to run the component on top of Globus, thus, freeing the non-grid-expert user from dealing with grid middleware. Instead of writing data distribution procedures and configuring the middleware appropriately for every new algorithm, Alignment HOC users reuse the existing component and only write application-specific plugins. To maintain plugins persistently in a reusable manner, we built a web-accessible plugin database with a comfortable administration GUI. The flexible component-based implementation makes it easy to study CPs in other databases (e.g. UniProt/Swiss-Prot) or to use an alignment algorithm different than the standard Needleman-Wunsch. For the efficient distribution of workload, we developed a library of group communication operations for HOCs.

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Metadaten
Author:Jan DünnweberORCiDGND, Philipp Lüdeking, Sergei GorlatchORCiDGND
DOI:https://doi.org/10.1007/978-0-387-78448-9_28
ISBN:978-0-387-78447-2
Parent Title (English):Making Grids Work
Publisher:Springer
Place of publication:Boston, MA
Editor:Marco Danelutto, Paraskevi Fragopoulou, Vladimir Getov
Document Type:Part of a Book
Language:English
Year of first Publication:2007
Release Date:2021/11/10
Tag:genome processing; higher-order components; middleware; sequence alignment
First Page:351
Last Page:362
Konferenzangabe:Proceedings of the CoreGRID Workshop on Programming Models Grid and P2P System Architecture Grid Systems, Tools and Environments 12-13 June 2007, Heraklion, Crete, Greece
Institutes:Fakultät Informatik und Mathematik
Fakultät Informatik und Mathematik / Labor Parallele und Verteilte Systeme
Publication:Externe Publikationen
research focus:Digitalisierung