Building Confidence in Quantitative Systems Pharmacology Models : An Engineer's Guide to Exploring the Rationale in Model Design and Development

This tutorial promotes good practice for exploring the rationale of systems pharmacology models. A safety systems engineering inspired notation approach provides much needed rigor and transparency in development and application of models for therapeutic discovery and design of intervention strategies. Structured arguments over a model's development, underpinning biological knowledge, and analyses of model behaviors are constructed to determine the confidence that a model is fit for the purpose for which it will be applied

Automated, Systematic and Parallel Approaches to Software Testing in Bioinformatics

Software quality assurance becomes especially critical if bioinformatics tools are to be used in a translational medical setting, such as analysis and interpretation of biological data. We must ensure that only validated algorithms are used, and that they are implemented correctly in the analysis pipeline – and not disrupted by hardware or software failure. In this thesis, I review common quality assurance practice and guidelines for bioinformatics software testing. Furthermore, I present a novel cloud-based framework to enable automated testing of genetic sequence alignment programs. This framework performs testing based on gold standard simulation data sets, and metamorphic testing. I demonstrate the effectiveness of this cloudbased framework using two widely used sequence alignment programs, BWA and Bowtie, and some fault-seeded ‘mutant’ versions of BWA and Bowtie. This preliminary study demonstrates that this type of cloud-based software testing framework is an effective and promising way to implement quality assurance in bioinformatics software that is used in genomic medicine