Date of Award


Document Type

Doctoral Thesis

Degree Name

Doctor of Philosophy


Computer Science

First Advisor

Prof Paul Walsh

Second Advisor

Prof Roy Sleator


This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And can this be done without placing an extra burden on an already multidisciplinary field of study? This is answered by reasoned argument with reference to current literature, and by experiment through a series of proof of concept implementations and their related published papers. In addition, a case study is presented where software engineering processes and technologies are used in a number of bioinformatic projects, and from this a novel taxonomy of the roles of code in bioinformatics is constructed. The conclusion is firstly that the application of software engineering elements from the two categories named above enhances reproducibility and scalability in bioinformatics, and secondly, that an intelligent integration of software engineering as a service into bioinformatics research, informed by the aforementioned taxonomy, is possible. Having demonstrated both efficacy and feasibility, this thesis concludes by recommending ways in which bioinformatic research teams move towards such integration.


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Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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