BioSIMP: Using Software Testing Techniques for Sampling and Inference in Biological Organisms

Mikaela Cashman, Jennie L. Catlett, Myra B. Cohen, Nicole R Buan, Zahmeeth Sakkaff, Massimiliano Pierobon, Christine A Kelley

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Years of research in software engineering have given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we reverse the direction and present BioSIMP, a process that models and predicts the behavior of biological organisms to aid in the emerging field of systems biology. It utilizes techniques from testing and modeling of highly-configurable software systems. Using both experimental and simulation data we show that BioSIMP can find important environmental factors in two microbial organisms. However, we learn that in order to fully reason about the complexity of biological systems, we will need to extend existing or create new software engineering techniques.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE/ACM 12th International Workshop on Software Engineering for Science, SE4Science 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2-8
Number of pages7
ISBN (Electronic)9781538627914
DOIs
Publication statusPublished - Jun 29 2017
Event12th IEEE/ACM International Workshop on Software Engineering for Science, SE4Science 2017 - Buenos Aires, Argentina
Duration: May 22 2017 → …

Publication series

NameProceedings - 2017 IEEE/ACM 12th International Workshop on Software Engineering for Science, SE4Science 2017

Other

Other12th IEEE/ACM International Workshop on Software Engineering for Science, SE4Science 2017
CountryArgentina
CityBuenos Aires
Period5/22/17 → …

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Keywords

  • Highly-Configurable Software
  • Systems Biology

ASJC Scopus subject areas

  • Computer Science Applications
  • Software

Cite this

Cashman, M., Catlett, J. L., Cohen, M. B., Buan, N. R., Sakkaff, Z., Pierobon, M., & Kelley, C. A. (2017). BioSIMP: Using Software Testing Techniques for Sampling and Inference in Biological Organisms. In Proceedings - 2017 IEEE/ACM 12th International Workshop on Software Engineering for Science, SE4Science 2017 (pp. 2-8). [7964305] (Proceedings - 2017 IEEE/ACM 12th International Workshop on Software Engineering for Science, SE4Science 2017). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SE4Science.2017.9