Title: Towards End User Interpretability of Configurable Software in the Biosciences
Abstract: End users of bioinformatics software tools range from bench scientists with little computational experience, to sophisticated developers. This diverse set of end users utilize applications for automating tasks to make decisions and draw scientific conclusions based on their discoveries. As the number and types of tools are increasing, they are also increasing in flexibility. The customization of these tools indicates bioinformatics is entering a mature phase of software development — that of highly-configurable software — where the end user is provided with many customization options. At the same time, biologists and chemists are engineering living organisms in a process that mimics software development. As they share their designs and promote re-use and plug-and-play, their programs are also emerging as highly-configurable.In this proposal we address two areas of configurability in the biosciences: (1) configurability of bioinformatics software, and (2) configurability of synthetic biology constructs. We highlight the challenges of configurability in these areas and provide approaches to help end users navigate the configuration spaces. First, we demonstrate there is variability in both the functional and performance outcomes of highly-configurable bioinformatic tools, discuss the implications of this variability, and provide suggestions for developers. We then define a mapping of software product line engineering to the domain of synthetic biology resulting in organic software product lines. In a case study we demonstrate the potential reuse and existence of both commonality and variability in an open source synthetic biology repository. We build feature models for two biological functions and demonstrate how product line engineering can benefit synthetic biologists. Proposed work includes developing algorithms to help bioinformatics users navigate the configuration landscape of scientific tools, and providing domain specific environments to help synthetic biologists reason about configurability in their applications.
Committee: Myra Cohen (major professor), Samik Basu, Robyn Lutz, Julie Ann Dickerson, James Lathrop