Navigating the maze: The impact of configurability in bioinformatics software

Mikaela Cashman; Myra B. Cohen; Priya Ranjan; Robert W. Cottingham

doi:10.1145/3238147.3240466

Navigating the maze: The impact of configurability in bioinformatics software

Mikaela Cashman, Myra B. Cohen, Priya Ranjan, Robert W. Cottingham

Computational and Predictive Biology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

18 Scopus citations

Abstract

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.

Original language	English
Title of host publication	ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering
Editors	Christian Kastner, Marianne Huchard, Gordon Fraser
Publisher	Association for Computing Machinery, Inc
Pages	757-767
Number of pages	11
ISBN (Electronic)	9781450359375
DOIs	https://doi.org/10.1145/3238147.3240466
State	Published - Sep 3 2018
Event	33rd IEEE/ACM International Conference on Automated Software Engineering, ASE 2018 - Montpellier, France Duration: Sep 3 2018 → Sep 7 2018

Publication series

Name	ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering

Conference

Conference	33rd IEEE/ACM International Conference on Automated Software Engineering, ASE 2018
Country/Territory	France
City	Montpellier
Period	09/3/18 → 09/7/18

Funding

This work is supported in part by NSF grant CCF-1745775 and by the Office of Biological and Environmental Research’s Genomic Science program within the U.S. Department of Energy Office of Science, award number DE-AC05-00OR22725.

Funders	Funder number
Office of Biological and Environmental Research
U.S. Department of Energy Office of Science	DE-AC05-00OR22725
National Science Foundation	CCF-1745775, 1901543, 1745775

Keywords

Bioinformatics
Configurability
Software testing

Access to Document

10.1145/3238147.3240466

Cite this

Cashman, M., Cohen, M. B., Ranjan, P., & Cottingham, R. W. (2018). Navigating the maze: The impact of configurability in bioinformatics software. In C. Kastner, M. Huchard, & G. Fraser (Eds.), ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering (pp. 757-767). (ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering). Association for Computing Machinery, Inc. https://doi.org/10.1145/3238147.3240466

Cashman, Mikaela ; Cohen, Myra B. ; Ranjan, Priya et al. / Navigating the maze : The impact of configurability in bioinformatics software. ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering. editor / Christian Kastner ; Marianne Huchard ; Gordon Fraser. Association for Computing Machinery, Inc, 2018. pp. 757-767 (ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering).

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abstract = "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.",

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Cashman, M, Cohen, MB, Ranjan, P & Cottingham, RW 2018, Navigating the maze: The impact of configurability in bioinformatics software. in C Kastner, M Huchard & G Fraser (eds), ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering. ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering, Association for Computing Machinery, Inc, pp. 757-767, 33rd IEEE/ACM International Conference on Automated Software Engineering, ASE 2018, Montpellier, France, 09/3/18. https://doi.org/10.1145/3238147.3240466

Navigating the maze: The impact of configurability in bioinformatics software. / Cashman, Mikaela; Cohen, Myra B.; Ranjan, Priya et al.
ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering. ed. / Christian Kastner; Marianne Huchard; Gordon Fraser. Association for Computing Machinery, Inc, 2018. p. 757-767 (ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Cashman M, Cohen MB, Ranjan P , Cottingham RW. Navigating the maze: The impact of configurability in bioinformatics software. In Kastner C, Huchard M, Fraser G, editors, ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering. Association for Computing Machinery, Inc. 2018. p. 757-767. (ASE 2018 - Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering). doi: 10.1145/3238147.3240466

Navigating the maze: The impact of configurability in bioinformatics software

Abstract

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Funding

Keywords

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