An open framework for extensible multi-stage bioinformatics software

G. Keeble-Gagnère; J. Nyström-Persson; M.I. Bellgard; K. Mizuguchi

doi:10.1007/978-3-642-34123-6_10

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An open framework for extensible multi-stage bioinformatics software

Journal article

Open access

Peer reviewed

An open framework for extensible multi-stage bioinformatics software

G. Keeble-Gagnère, J. Nyström-Persson, M.I. Bellgard and K. Mizuguchi

Pattern Recognition in Bioinformatics, Vol.7632(7632), pp.106-117

2012

DOI: https://doi.org/10.1007/978-3-642-34123-6_10

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Abstract

In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance. Performance-sensitive tools are often highly monolithic, which can make research difficult. We present a novel set of software development principles and a bioinformatics framework, Friedrich, which is currently in early development. Friedrich applications support both early stage experimentation and late stage batch processing, since they simultaneously allow for good performance and a high degree of flexibility and customisability. These benefits are obtained in large part by basing Friedrich on the multiparadigm programming language Scala. We present a case study in the form of a basic genome assembler and its extension with new functionality. Our architecture has the potential to greatly increase the overall productivity of software developers and researchers in bioinformatics.

Details

Title: An open framework for extensible multi-stage bioinformatics software
Authors/Creators: G. Keeble-Gagnère (Author/Creator) - Murdoch University
J. Nyström-Persson (Author/Creator) - National Institute of Biomedical Innovation, Health and Nutrition
M.I. Bellgard (Author/Creator) - Murdoch University
K. Mizuguchi (Author/Creator) - National Institute of Biomedical Innovation, Health and Nutrition
Publication Details: Pattern Recognition in Bioinformatics, Vol.7632(7632), pp.106-117
Publisher: Springer-Verlag
Identifiers: 991005542704607891
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article
Note: Paper presentation at the 7th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2012; Tokyo; 8 November 2012 - 10 November 2012

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