Project Description

Dr Joshua W.K. Ho

 

Head, Bioinformatics and Systems Medicine Laboratory
Victor Chang Cardiac Research Institute

Bioinformatics software testing and quality assurance

Bioinformatics methods, models and applications to disease

Wednesday 6 July 2016

Joshua Ho completed a BSc (Hon 1, Medal) in Biochemistry and Computer Science in 2006 and a PhD in Bioinformatics in 2010, both from the University of Sydney. He then completed an interdisciplinary postdoctoral fellowship at the Harvard Medical School (HMS), and was promoted to an Instructor in Medicine in 2012. In 2013, he returned to Australia to set up the Bioinformatics and Systems Medicine Laboratory at the Victor Chang Cardiac Research Institute. Joshua is also an NHMRC/National Heart Foundation Career Development Fellow, and a conjoint senior lecturer at UNSW. In 2015, he was awarded the NSW Ministerial Award for Rising Stars in Cardiovascular Research, and the Australian Epigenetics Alliance’s Illumina Early Career Research Award. His research focuses on developing fast and reliable bioinformatics methods to identify the genetic cause of inherited heart diseases, using a range of approaches such as whole genome sequencing, machine learning, systems biology, cloud computing, and software testing and quality assurance.

Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Arguably the main research focus has so far been on the computational and statistical basis of the algorithms. Surprisingly much less effort has been placed on the quality of the design and implementation of these algorithms – even though clearly correct design and implementation of the underlying algorithm is at least as important as the algorithm itself. Incorrectly computed results may lead to wrong biological conclusions, and subsequently misguide downstream experiments. This problem is especially critical if these bioinformatics tools are to be used in a translational clinical setting. In this lecture, we will discuss key concepts and methods in the field of software testing. We believe introducing and adapting state-of-the-art software testing and quality assurance techniques in bioinformatics is a critical step in improving the quality, reproducibility, and accountability of bioinformatics tools.