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Title: Navigating the maze: the impact of configurability in bioinformatics software
The bioinformatics software domain contains thousands of applications for automating tasks such as the pairwise alignment of DNA sequences, building and reasoning about metabolic models or simulating growth of an organism. Its end users range from sophisticated developers to those with little computational experience. In response to their needs, developers provide many options to customize the way their algorithms are tuned. Yet there is little or no automated help for the user in determining the consequences or impact of the options they choose. In this paper we describe our experience working with configurable bioinformatics tools. We find limited documentation and help for combining and selecting options along with variation in both functionality and performance. We also find previously undetected faults. We summarize our findings with a set of lessons learned, and present a roadmap for creating automated techniques to interact with bioinformatics software. We believe these will generalize to other types of scientific software.  more » « less
Award ID(s):
1901543 1745775
PAR ID:
10097964
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering - ASE 2018
Page Range / eLocation ID:
757 to 767
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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