Supporting computational systems science: genomic analysis tool federations using aspects and AOP

Authors:
David Stotts;Keith Lee;Ivan Rusyn
Affiliations:
Department of Computer Science, and School of Public Health, University of North Carolina at Chapel Hill;Department of Computer Science, and School of Public Health, University of North Carolina at Chapel Hill;Department of Computer Science, and School of Public Health, University of North Carolina at Chapel Hill
Venue:
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Year:
2008

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Abstract

We show how Aspect-Oriented Programming (AOP) and its mainconcept - the aspect - can be used to effectively construct interoperating collectionsof scientific tools and models. Such collections, termed "federations",naturally arise in computational frameworks for bioinformatics problems. Programmingmodern scientific simulations and models require more domain expertisethan can be found in one researcher; often the many researchers neededto create the various computational components of a full solution cannot begathered to work as a single controlled software development team. Our approachallows individuals to construct their own components and tools, andthen have them assembled without alteration (and without coordination of theoriginal programmers) into a federation for the larger final computational solutions.We illustrate the methods with two SNP and haplotype analysis toolswritten in Python.