An open framework for extensible multi-stage bioinformatics software
Keeble-Gagnère, G., Nyström-Persson, J., Bellgard, M.I. and Mizuguchi, K. (2012) An open framework for extensible multi-stage bioinformatics software. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7632 (7632). pp. 106-117.
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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.
|Publication Type:||Journal Article|
|Murdoch Affiliation:||Centre for Comparative Genomics|
|Copyright:||© 2012 Springer-Verlag|
|Notes:||Paper presentat at the 7th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2012;Tokyo;8 November 2012-10 November 2012|
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