Genomics Aotearoa

Licensing bonanza in computational life sciences*   - Genomics Aotearoa

Sep 09, 2021

By Florian Pichlmueller (University of Auckland) and Christina Straub (ESR) . 2min read GPL, MIT, BSD, CC – no they’re not a secret vocabulary, these are in fact acronyms for open source licenses that allow code to be freely used, modified and shared. And there are many more – take a look at the open source initiative to see a whole new world. Believe it or not there’s even a code acronym called WTFPL which stands for “Do What The F*** You Want To Public License.” Software licenses are a topic that receives little attention by researchers when it comes to making our own code public. But with the ever-increasing amounts of computational analysis of ‘omics data and the aim of data reproducibility and code sharing in the scientific publishing world, an appropriate open-source license should be included … Read More

Understanding life in our waterways through metagenomics - Genomics Aotearoa

Sep 03, 2021

By Michael Hoggard and Carmen Astudillo Garcia, University of Auckland The rapid development and extraordinary cost reductions of next-generation sequencing technologies has greatly increased data on the functioning of complex microbial communities. Although relatively new, metagenomics has already dramatically influenced our understanding of the microbial tree of life and the known virosphere via the genomic traces of organisms and viruses that have otherwise not been previously observable. What is metagenomics? Techniques that explore microorganisms have evolved in the past decades, from microbial culture techniques to single gene amplification and sequencing. And now whole-genome analysis (genomics) provides a more comprehensive, integrated approach to understanding single microbial function and physiology. But more recently, a metagenomic approach can directly analyse all genomes contained in an environmental sample as a way to understand the functional gene composition of entire microbial communities.  This gives … Read More

Genomic solutions for a plant taonga: a high-quality rewarewa genome - Genomics Aotearoa

Jun 09, 2021

[Illustration credit: “Seven Sisters, Knightia excelsa” Jennifer Duval-Smith ] By Plant & Food Research High Quality Genomes project co-leader David Chagné The completion of the native rewarewa (Knightia excelsa) tree genome sequence is demonstrating New Zealand is now taking charge of producing genomes on its native species. These are species that are important to us, and have taonga significance. Rewarewa tree. Credit: Alex Fergus The completion of the genome sequencing of the rewarewa by our team of Manaaki Whenua – Landcare Research, Plant & Food Research and University of Otago scientists is a really good example of the sequence now being available to use for the benefit of New Zealand. The Genomics Aotearoa-funded research, led by Genomics Aotearoa postdoctoral researcher Ann McCartney, has developed a great set of techniques benchmarking genomic solutions which is precious and useful … Read More

Indigenous Genomic Databases – two case studies - Unsorted

May 26, 2021

By Phillip Wilcox, University of Otago, Ngāti Rakaipaaka, Rongomaiwahine, Ngāti Kahungunu ki te Wairoa There is no one size fits all when it comes to designing research that fulfils cultural obligations, but two research exemplars from opposite ends of the world that incorporate Indigenous perspectives are providing potential direction. It’s hoped exemplars such as these will be able to guide the design of databases and more culturally safe and relevant study designs that address the lack of genetic data on Indigenous populations currently hindering genetic diagnosis in health. Improving access to the benefits from precision medicine, including tailored treatment for genetic disorders, will help to correct existing inequities that are often referred to the ‘genomic divide’. This lack of population-specific information is a global issue, attributed to a poor understanding and acknowledgement from many researchers of valid concerns around sampling … Read More

Where are all the four-leaf clovers? And what does that have to do with learning to code? - Genomics Aotearoa

Mar 30, 2021

By Monica Vallender, Master’s student with AgResearch Invermay and the University of Otago. A few months ago, while home for the Christmas break, my mother – out of the blue – turned to me and asked, “what made you actually decide you wanted to go to university and study science?” Shocked and never thinking that I would someday have to explain my choice, I replied saying “honestly, no one ever told me I couldn’t.” I never really considered that no one else in our family had done that before. I come from a stereotypical kiwi family – my family was working class, which meant that sometimes over summer, I’d get to spend a few weeks on a farm in the middle of nowhere with an aunt or a second cousin to “keep me out of trouble.” What I never appreciated … Read More

Wasps are forever? The potential to eliminate an invasive pest in New Zealand; permissions withstanding - Genomics Aotearoa

Dec 21, 2020

By Gemma McLaughlin, University of Otago PhD candidate Invasive social wasps have long plagued New Zealand’s beech forests and suburbs. Now, a  genetic technology holds the potential to stop such wasps in their tracks. But one major issue lurks: are scientists even allowed to explore this option? New Zealand summers are a great thing. We have our kiwi classics: the barbecues, the beaches, the roadie. But we also have a less than welcome visitor that can serve as a source of irritation or just a downright disruption to the festivities; the social wasp. These winged nuisances thrive in our environment, with densities higher here than anywhere else in the world – not really something we can brag about! And while they can be an annoyance for us, they are a much bigger problem for other species residing here. Native caterpillars … Read More

Changing stuff… - Genomics Aotearoa

Nov 25, 2020

By Professor Peter Dearden, Director Genomics Aotearoa Science is an excellent way of allowing us to question test and understand the world we live in. But that knowledge also provides us with something else; the ability to change things, to solve problems, and to make life on earth a bit better. This is clearly the case in medicine; by understanding a disease, and the way it interacts with the body, we can find ways to intervene, to improve outcomes and perhaps find a cure. And it is commonplace in other sciences; problems of mass communication are solved with electronics, lightweight batteries and radio waves, leading to the cell phone in your hand, and the remarkable changes in our society these devices have caused. This is the role of science, not just to understand, but to improve and … Read More

Indigenous perspectives on unrestricted access to genomic data - Genomics Aotearoa

Sep 23, 2020

By Genomics Aotearoa researcher Maui Hudson, University of Waikato It is vital that genomics research respects genomic data and genetic heritage from indigenous communities. Genomics research is a rapidly growing field of study, and there is a strong push to make the huge amount of data being produced open source for all researchers to use – the rational being that more available science creates greater societal benefits. But we know that isn’t actually the case, and that unrestricted access to genomics data can lead to injustice. We –  myself and a group of New Zealand from the University of Waikato, University of Otago and University of Canterbury, Crop and Food Research and Manawaora The Centre for Health, Tauranga, teamed up with international researchers from prominent research organisations in the United States, Canada, Australia, South Africa and Spain to delve … Read More

Tackling the hard issues – trust and relationships - Genomics Aotearoa

Sep 15, 2020

By Claire Grant, Genomics Aotearoa Communications Manager Community consultation is becoming an increasingly important aspect of research programmes in New Zealand, and with that comes the art of relationship building. Engagement between scientists and user-groups is certainly nothing new. But as stakeholder involvement becomes more of a requirement for science, it becomes harder to define what constitutes effective consultation, and what a community partnership looks like in practice. And that has implications for our traditional skill sets – it’s no longer simply packaging science through education and disseminating published science results. It requires a meaningful relationship. Engagement is not a tradition taught subject and may not necessarily be something we’re all good at. But I’d argue we could stop thinking of “soft skills” as an add-on, and instead consider them a list essential for career success.  In other words, we … Read More

Containers for reproducible bioinformatics research - Genomics Aotearoa

Aug 12, 2020

By Aleksandra Pawlik, Ngoni Faya, Joseph Guhlin, Megan Guidry, Tom Harrop, Dinindu Senanayake Rapid development of computational bioinformatics tools mean we can more easily push research boundaries. However, it comes at a cost. The complexity of the software chain that needs to be installed and configured to run advanced workflows results in researchers spending hours, if not days, trying to set up and debug the computational environment before they can even start to analyse their data. Complex setups also hinder reproducibility, one of the core principles of science. Fortunately, there is a solution growing in popularity – containers. Simply put, containers allow wrapping up software packages in an executable environment which can be moved from one computer to another regardless of which operating system these computers run. You can think of it as a “computer inside a computer”, contained … Read More