Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

Abstract

There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

Keywords: bioinformatics; microbial biotechnology; process; software; software engineering; survey.

Figure 1.

Key Components of Software Engineering.

Figure 2.

Responses to questions on infrastructure.

Figure 3.

Responses to questions on processes.

Figure 4.

Responses to questions on practices.

Figure 5.

Responses to questions on goals.

Figure 6.

Suggested project Roles of bioinformaticians and bioinformatic engineers.

Figure 7.

Handover points between bioinformaticans and bioinformatic engineers.