Deputy Director – Auckland Bioengineering Institute
Deputy Director – The Medical Technologies CoRE
Associate Deputy Vice-Chancellor (Research) PBRF – The University of Auckland
Professor Merryn Tawhai is the Deputy Director of the Auckland Bioengineering Institute, University of Auckland, and Deputy Director of the Medical Technologies Centre of Research Excellence. Merryn’s research is in computational respiratory physiology, developing anatomically-detailed models of the lung that span cell-to-organ function. She was awarded the 2016 RSNZ MacDiarmid Medal for “outstanding scientific research which demonstrates potential for human benefit”.
Creating a personal digital lung
There are currently very few tools for quantitative assessment of the lung prior to surgery, radiation treatment, or other interventions. Current tools focus on image analysis, usually based on densitometry or texture analysis. No tools are currently available for patient-specific prediction of respiratory system function post-treatment. We are developing a digital lung model that provides the capability to predict redistribution of air and blood flows and their impact on gas exchange and other physiological functions in response to various interventions or treatments. The digital lung spans from the nasal and oral airways to the deepest smallest parts of the lung, connects to the circulatory system, exchanges respiratory gases, and interacts with models for central and peripheral respiratory control. A lean version of the model provides rapid analysis of breath-by-breath data at the bedside, and higher fidelity versions of the model provide deep analysis of patient response to treatment. Inclusion of imaging and pulmonary function data from hundreds of normal healthy subjects means that the model appropriately represents structure-function relationships over the full adult lifespan. We now have a full personalisable model that has the capability to link 3D imaging (MRI or PET of ventilation defects) to forced expiration (the mainstay of pulmonary function testing) and other laboratory tests that are more sensitive to ventilation heterogeneity. The ultimate goal is to provide a comprehensive tool that can be used to predictively test interventional approaches and therapies, both well in advance and at the bedside, to develop and optimise new and current treatments for the individual, as well as to identify and stratify patients into risk groups and groups in need of more targeted, personalised therapies.
Head of Research Software Development – Research IT Services, UCL
Head of Research Engineering – The Alan Turing Institute
A growing proportion of researchers carry out their research through the medium of computer code, whether in traditional programming languages, or in domain specific languages used by modelling platforms. Such research often suffers through the lack of software development best practice within research teams. While postdocs and PhD students often do not have the time, and are not incentivised, to produce high-quality software usable by other researchers and sustainable beyond the lifetime of a project, generic contract software developers are not equipped to understand the academic context of the research. In the UK, a solution has emerged since 2012 in the form of a new kind of research professional: the Research Software Engineer combines the knowledge and expertise of a computational scientist with the values of a professional software engineer.
Dr James Hetherington is one of the founders of the RSE movement in the UK, and created the first university-based RSE group in 2012 in UCL. He is now Head of Research Engineering at the Alan Turing Institute, the UK’s national institute for Data Science, and of Research Software Development at UCL. Across these two institutions, he leads a team of twenty research software engineers and data scientists contributing to a huge range of data- and compute-intensive research.
He advocates that readable, reliable and efficient software, written for humans to understand as well as computers to execute, forms an important part of research communications and can deliver significant research impact, and his team works with researchers in many different fields to put this into practice. James has been instrumental in establishing the role of the Research Software Engineer as a recognised career path in the UK science system and in promoting the value of research software as a first-class research output. He aims to build a stable home for research programmers within research institutions, and to secure for research the benefits of the high-quality software they write.
“The Craftsperson and The Scholar”: Research Software Engineers, Data Scientists, and multi-professionalism in e-Research.
Since 2012, the UK has been experimenting with a new professional role in Academia – the Research Software Engineer. We conjecture that the profound sustainability, quality, correctness and reproducibility problems we perceive in computationally based research arise in part due to the incentive structures under which programming postdocs operate. By defining a new role, part of the academic community, but with different career objectives focused on software quality and impact, we believe we have hit upon a critical component of the solution, leading to more readable, reliable, efficient and sustainable research software.
Research Software Engineering groups now exist in many of the UK’s leading research-intensive universities, a number of research council RSE Fellowships have been appointed, and over 200 people attended our second annual conference this year. We are now exploring how this model might work for other parts of the interdisciplinary research team needed for 21st century research, and are including specialist Data Scientists in RSE groups.
Professor Marina Jirotka
Professor – Human Centred Computing, Department of Computer Science
Associate Director – e-Research Centre at the University of Oxford
Marina Jirotka is Professor of Human Centred Computing in the Department of Computer Science and Associate Director of the e-Research Centre at the University of Oxford. She leads an interdisciplinary research group investigating the responsible development of ICT. Her research has long been concerned with bringing a richer understanding of work practice into the process of engineering technological systems. Early in her career, she helped develop the use of video-based ethnographies in Requirements Engineering which she drew upon later in her research on e-Research applications in a wide variety of projects, including studies involving applications in e-Health, e-Science and e-Humanities. In these studies, Marina was concerned with how technologies could be developed to be sensitive to the interpretative practices of scholars and scientists, support forms of collaborations between practitioners, and help maintain trust built up between participants.
In developing innovative solutions to particularly complex problems, these projects raised a general set of issues for the participants for example, regarding how data could be shared, how data could be reused in different settings, and how digital archives raised many challenges at the institutional, disciplinary and personal level where researchers found themselves caught between conflicting requirements. These issues, though often characterised as ‘social or ethical’, raised concerns that are much broader than those usually considered in formal ethical procedures. To try and unpack and address such issues, Marina has been at the forefront of recent research in Responsible Research and Innovation (RRI) in both the UK and the European Union. Her current projects involve a range of topics in RRI: she leads the Responsible Innovation initiative for Quantum Technologies; she has co-developed a social charter for embedding novel platforms into Smart Societies; and from her work on the spread of hate speech and misinformation on social media, she has recently been appointed specialist advisor to the UK House of Lords Select Committee on Communications for their inquiry into Children and the Internet.
“I don’t think I’ve come across an unethical scientist”
At a time when powerful technologies have the potential to transform society, investigators in all fields are under growing pressure to consider the motivations, purposes, and possible consequences associated with their research. Almost daily there are examples where ICT grabs the headlines about the potential consequences of recent innovations. These issues typically are raised only after the technologies have been introduced into mainstream use. Whilst developments in science and technology have always run ahead of our ability to think through their ethical implications, the rate of change seems to be accelerating. A novel initiative called “responsible research and innovation,” (RRI) has emerged recently in response to the challenge of designing innovation in a socially desirable and acceptable way. This approach may be useful for framing the discussion about how to manage the introduction of future ICT innovations.
In this talk, I will trace the roots of Responsible Research and Innovation in ICT and demonstrate connections to recent work in e-‐Research. Many of the attempts to make the vision of global, multi-‐disciplinary, collaborative research and data sharing a reality at ground level have given rise to a raft of unanticipated ethical, social and institutional concerns. I will discuss these and some of the theoretical and methodological challenges of embedding RRI into researchers’ development practices and conclude with some practical and innovative approaches to deploying RRI.
Dr Allan McRae
NHMRC Career Development Fellow, Institute for Molecular Bioscience
Joint Appointment, Queensland Brain Institute
Dr Allan McRae obtained a BSc in Statistics from the University of Otago and then a PhD in Quantitative Genetics from the University of Edinburgh. In 2006 he joined the Queensland Institute of Medical Research, before moving to the University of Queensland in 2012.
He currently leads the Systems Genomics theme in the Program in Complex Trait Genomics at the Institute for Molecular Bioscience. His research group focuses on the understanding of genetic and environmental control of variation in low level biological traits, including DNA methlyation and gene expression, and how this can inform our understanding of complex disease.
Genomic Basis of Human Disease
The last decade has seen an explosion in the discovery of DNA variants associated with disease or other complex traits. The challenge for the next decade is to identify the causal genetic variants underlying these associations and biological mechanism that affect disease risk. To achieve this goal, researchers are taking systems level approach by combining genetic data with a variety of low-level genomic measures including gene-expression and DNA methylation. This talk will introduce a range of genomic data and how we are using this data to better understand the genetic and environmental contribution to human complex traits and disease.
Senior Head of Technology & Research – Weta Digital
Luca Fascione is Senior Head of Technology & Research at Weta Digital, where he oversees Weta’s core R&D efforts including Simulation and Rendering Research, Software Engineering and Production Engineering.
Luca is the lead architect of Weta Digital’s next-generation proprietary renderer, Manuka. This renderer is the culmination of a three-year research endeavour involving over 40 researchers and continues to allow Weta Digital to produce highly complex images with unprecedented fidelity.
Luca joined Weta Digital in 2004 and has also worked for Pixar Animation Studios. Through a partnership with NVIDIA, Luca co-developed the GPU-based PantaRay that was instrumental in the making of the movie Avatar, and (since 2011’s The Adventures of Tintin) also became the foundation of volumetric shadow support within the Weta pipeline. Luca was recently recognized with a Scientific and Engineering award from the Academy of Motion Pictures for his work on FACETS, Weta’s facial motion capture system.