Fostering best practice and increasing global research collaboration by transitioning researchers to more powerful and flexible analysis platforms
Marine science is driving the development of Australia’s “blue” economy.
Part of Nectar’s Australian Science Cloud initiatives, the Marine Sciences Cloud provides a framework of easily-accessible cloud-based tools and resources to support marine and climate science community research into the ocean, its habitats, ecosystems and life forms, as well as the study of coastal environments, oceanic currents and the sea floor.
“We wanted to increase engagement for the Australian and international marine and climate science community by providing access to cloud-based tools for data analysis and data manipulation.” according to Roger Proctor, Director – Australian Ocean Data Network – part of the NCRIS capability IMOS – Integrated Marine Observation System.
“The Marine Sciences Cloud is an Australian-led opportunity to conduct internally-recognised activities that are also internationally collaborative” says Roger. “It is obvious that these kinds of research cloud activities will significantly assist the advancement of Australian research.”
“The Australian Science Clouds provides a new model for delivering eResearch infrastructure through strategic partnerships with NCRIS research-domain capabilities.” According to Dr Glenn Moloney, Nectar Director.
“The Science Clouds initiative enables us to bring together all the key parties in each domain to have a framework for collectively discussing and shaping the Research Cloud environment for each domain, and for bringing together the data, tools and infrastructure to meet national and community priorities.” continues Kheeran Dharmawardena, Coordinator of the Science Clouds project at Nectar.
The Marine Sciences Cloud
The Marine Sciences Cloud comprises two key elements – a suite of tools accessed via a Virtual Desktop hosted on Nectar infrastructure, as well as a national service for annotating and analysing underwater imagery. The annotation and analysis service includes SQUIDLE+ for analysis and classification, and GlobalArchive that provides a platform for sharing, cataloging and exploring archived annotation data.
Researchers now hit the ground running – Virtual Desktop
“The Marine Sciences Cloud Virtual Desktop is an incredible time saver – it enables researchers to hit the ground running”
Lack of technical information technology literacy is one of the greatest challenges faced by researchers. While researchers are understandably highly skilled in techniques related to their specific research domains, there is an ever-increasing requirement to also possess high-level IT skills. While experienced researchers are often well-versed in IT matters, other researchers – especially novice researchers – are challenged by the technical overhead required to use existing research initiatives such as the Nectar Cloud.
Rather than undertaking research and analysis activities, researchers often need to first overcome IT challenges such as accessing a dashboard, launching virtual machines, loading software to suit their specific needs – before finally being able to conduct their research and analysis activities.
“The Marine Sciences Cloud Virtual Desktop is an incredible time saver – it enables researchers to hit the ground running” states Brendan Davey, Deputy Director at TPAC – the Tasmanian Partnership for Advanced Computing. “We were especially keen to ease the way for first time users and are excited that these researchers can now be up and running within 2 minutes using the Virtual Desktop”.
The Virtual Desktop provides an easily-accessible environment that comes pre-installed with all the necessary tools (such as rstudio and ipython) to significantly reduce the timeframe for researcher access. Before Nectar’s Marine Sciences Cloud Virtual Desktop was established, experienced researchers using a handful of tools took around half a day to be in a position to perform analysis. This timeframe potentially extended to weeks for less experienced people to identify the required software and configure the environment to process data.
“The Virtual Desktop environment established as part of the Marine Cloud is leveraging and adapting the technology built by TERN for use in marine sciences. It is a good example of the inter-domain collaboration that the Science Cloud initiative from Nectar is fostering to make more effective use of the infrastructure investments that have been made.” said Kheeran.
“Transitioning researchers to more powerful and flexible analysis environments was also a determining factor” states Roger, “In order for researchers to link to more diverse data collections, it is imperative to transition away from desktop-bound tools.” Although desktop tools such as Excel spreadsheets have been the traditional mainstay for research analysis, the increase in the availability, complexity and size of datasets in current research environments has clearly flagged the need to use alternate tools to overcome current data capability issues – especially in the areas of data discovery, storage, management and sharing.
“The Marine Sciences Cloud paves the way for increased collaboration resulting from increased data access”
“The Marine Sciences Cloud paves the way for increased collaboration resulting from increased data access” states Roger. It provides the ability to link to existing data sources such as the globally-recognised IMOS data collections. To further increase tool accessibility, additional developments are currently underway to provide working examples and sample code that can be leveraged by researchers if required.
“Sector-wide collaboration was essential when determining the Marine Sciences Cloud requirements” says Roger. “Feedback from several institutions, including researchers from the Institute for Marine and Antarctic Studies, Antarctic Climate and Ecosystem Cooperative Research Centre, Australian Antarctic Division, helped us better understand how the Marine Sciences Cloud could address important barriers.”
“Complexity is a barrier to use for new researchers” according to Brendan. TPAC had already gained significant first-hand experience and valuable feedback in this space by running Nectar Cloud starter sessions for the institutions for the last few years. “We wanted to continue hosting these valuable workshops, but also wanted offer researchers something more user-friendly – and therefore more useable and useful.”
“The Marine Sciences Cloud Virtual Desktop is fostering best practice – providing researchers with a standard environment and standardised processes for accessing and using data” says Brendan.
With accessibility and future flexibility in mind, the key Marine Sciences Cloud components – namely the SQUIDLE+ annotation tool used to annotate georeferenced video and images, and the GlobalArchive online centralised metadata repository – were developed as free access platforms that leveraged lessons learned from earlier software versions and currently support all kinds of georeferenced imagery data.
“Longevity will be a natural outcome because the wider research community is contributing to these technologies” says Brendan Although many of the tools are similar, there are specialised items that provide uniqueness in terms of its connectivity into marine data and function. “With other Nectar Science Clouds keen to SQUIDLE+ and GlobalArchive, we will continue to see the development of a common analysis and storage environment.”
Looking forward, the team is keen to integrate activities so users can link from GlobalArchive to the virtual desktop and remotely access imagery. With the desktop environment already established, it will be relatively easy to broaden the scope of the analysis platforms by adding additional tools.
Both GlobalArchive and SQUIDLE+ run Application Programming Interfaces (APIs) in the background that allows the different services to communicate with each other and allow different tools on the research cloud to interface with each other to share data and perform other activities – without the need to download the data.
“Thanks to Nectar’s Science Cloud initiative, the Marine Sciences Cloud has delivered significant advances in collaboration and sustainability across the global marine science community.” According to Brendan “and we look forward to a bright future ahead”.
Nectar is pleased to be driving the development of the Marine Sciences Cloud. For more information, see https://nectar.org.au/science-clouds/.
Based on interviews with four leaders in the marine science community about the ground-breaking research impacts being advanced by the Nectar Marine Sciences Cloud:
- Dr Roger Proctor, Director – Australian Ocean Data Network – part of the NCRIS capability IMOS – Integrated Marine Observation System.
- Mr Brendan Davey, Deputy Director, Tasmanian Partnership for Advanced Computing (TPAC).
- Dr Ariell Friedman, SQUIDLE+ Lead Developer and Data Science Consultant, Greybits Engineering.
- Dr Tim Langlois, Lecturer, School of Biological Sciences and the Oceans Institute, University of Western Australia.
Story: Loretta Davis