Collaboration creates Aotearoa’s first publicly accessible genomics platform
A four-year collaboration between registered charity, Genomics for Aotearoa New Zealand, and local cloud providers, Catalyst Cloud, has created Aotearoa's first bioinformatics platform for use by independent genomics researchers. The platform not only democratises access to expensive processing infrastructure and bioinformatic data but also radically reduces the time, and cost, of undertaking important genomics work compared to other cloud-based solutions. It also helps to address the 'reproducibility crisis' in science, providing a transparent and easy way to reproduce and reuse analysis systems.
The low down
Genome scale research produces massive amounts of data that needs to be processed into something useful. In the past, it required a huge investment in computers and infrastructure, which limited this kind of work to large organisations. This is no longer true. Catalyst Cloud has been working with Genomics for Aotearoa New Zealand since 2017 to build the first public genomics platform and to cross train people in bioinformatics and cloud computing. Using open standards-based cloud computing, the tools and the infrastructure are available to anyone on an affordable pay-for-what-you-use basis. No more waiting in a queue for an unknown, and possibly lengthy, time for a high-performance computing cluster to become available to process the genomics data. This opens up a whole new world of possibilities for researchers and scientists.
The Genomics for Aotearoa New Zealand platform has been successfully tested on the Catalyst Cloud to support two separate genomics research projects - one to understand the genetic diversity in brown kiwi and the other to understand the genetic basis of flightlessness in birds.
Genomics work is vital to conserve brown kiwi, whose populations the Department of Conservation estimate are declining by 2 - 3% each year. The hapū -led Kiwi Whakapapa Project is working towards providing a more detailed understanding of genetic diversity in isolated groups of brown kiwi to help hapū and other decision-makers advance the goal of achieving diverse and successful kiwi populations for generations to come.
The bioinformatics platform was used with the population structure analysis software package, StructureThreader, to help understand the relatedness of North Island brown kiwi populations. Massey University Senior Lecturer and co-supervisor of the project, Simon Hills (Ngāti Porou), said "Because the Genomics for Aotearoa New Zealand platform is container based, we can share containers and workflows between users making them reproducible and reusable for future analyses -- saving time, energy, and money."
The genome assembly of flighted and flightless birds took researcher, Dr Gillian Gibb, about 2 days to run on the Catalyst Cloud, compared to 5 days a similar assembly took on an offshore cloud platform. This more efficient processing is due to the improved efficiency of the Catalyst Cloud Kubernetes platform and reduced latency. "The platform has allowed me to change the way I approach bioinformatics. I can experiment more because it is fast and inexpensive," said Gillian Gibb.
Open-source and open genomics
The cross-disciplinary project team has taken an open-source technology and open genomics approach to create as close to ideal as possible bioinformatics platform in the cloud. As a result, the collaboration has created a solution that both allows indigenous data to remain in Aotearoa and that makes access to processing power more readily available to genomics researchers than ever before, with access no longer dependant on a researcher's relationship to a particular institution.
World class scientific computing
Genomics for Aotearoa New Zealand President, Rob Elshire, said "The team at Catalyst Cloud have been instrumental in supporting the work we are doing in cloud computing. They have worked side by side with us since 2017 to make it all go". He went on to say, "The collaboration between Genomics for Aotearoa New Zealand and Catalyst Cloud shows that in Aotearoa we can achieve great outcomes using cloud for scientific computing on a par with the European Helix Nebula science cloud initiative."
Independent genomics researchers, here and overseas, can now benefit from a best practice, always available and affordable cloud computing platform for running complex bioinformatic processes. This has significant implications for better use of genomics in, for example, conservation and in farming here in Aotearoa, enabling more informed decision making in everything from native species recovery, to improved stock yields and reducing greenhouse gas emissions.
Benefits of Kubernetes
Genomics for Aotearoa New Zealand uses the Catalyst Cloud Kubernetes platform to deliver containerised bioinformatics applications. This use of containers has made automation of the complex processes much easier. Together with the project's use of the Argo Workflows application to transparently manage workflows, Kubernetes makes it possible to replicate the many different stages used in a bioinformatics process. The difficulty in exactly reproducing complex analyses has been an ongoing challenge in science. Overtime this improved reproducibility will allow better quality control in genomics, and more confidence in published results.
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