WAMSI Bulletin
More news about WAMSI and its partners in the latest WAMSI Bulletin.
WAMSI Bulletin
How can supercomputing help with marine science?
There’s no doubt that Big Data is one of those concepts that is completely transforming the way we do research but what other capability does a facility like the Pawsey Supercomputing Centre have that can help marine science?
In June, the Pawsey Supercomputing Centre is offering a range of free short courses on supercomputing topics. WAMSI researchers, partners and friends are encouraged to consider taking advantage of the courses on offer or contact WAMSI Data Manager Luke Edwards to find out more about exploring the potential of the Pawsey supercomputing capacity.
On 8-9 June, the sessions are aimed at those new to supercomputing (8th), and those wanting to understand more about using the systems (9th).
The largest of these systems is Magnus. It has over 35,000 cores, delivering in excess of 1PetaFLOP of computing power. It is the most powerful public research supercomputer in the Southern Hemisphere and debuted at #41 in the Top500 list. Marine researchers can apply for time on Magnus (details here). Magnus and other supercomputers are designed for highly parallel distributed programs.
Marine researchers who don’t have problems or software programs that can make use of Magnus should also be aware of the NeCTAR research cloud. It enables researchers to create VMs (virtual machines), similar to Amazon Web Services, and deploy research tools and software without having to run their own physical servers. This dramatically reduces the overhead for researchers to run research applications while allowing them to scale up or down the amount of processing power required.
One of the important parts of the WAMSI program is to ensure the data collected through research is protected in the longer term and held in a place where it can be accessed both for management and planning purposes.
WAMSI Data Manager Luke Edwards, is based at the Pawsey Supercomputing Centre. Its huge data storage capacity is available not just for radio astronomers linked to the Square Kilometre Array, but all researchers, including marine researchers.
With greater than 40 Petabytes of data storage available, researchers are encouraged to apply for storage if they have more than 5Tbs of data. The aim of the storage is to facilitate sharing and collaboration with research partners. To discover more about how to apply for storage visit here.
The Pawsey Supercomputing Centre Visualisation team can also provide a package of hardware, software and expertise that can assist marine researchers.
Applying visualisation techniques to difficult datasets can require specialist hardware, which can include high end graphics cards for handling large datasets in real-time, novel display technologies to fully exploit the human visual system, and user interface devices to facilitate the interaction. To find out more visit here.
“The big question raised by researchers is how do I best document my data so in ten years’ time (WAMSI 4), I can use all this great data from the Kimberley and the Dredging Node,” Mr Edwards said.
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| Source: http://imgs.xkcd.com/comics/documents.png |
“It’s the simple stuff that is the key to good data management, like making sure you have good conventions for file names and complete metadata,” he said.
WAMSI has a requirement that all data is made publicly available and therefore it’s important that its researchers make it discoverable through creating metadata.
“The big mistake researchers can make is to start off with a little bit of data not thinking they’ll need formal data management,” Mr Edwards said. “They might think they can handle it and back it up on a portable hard drive. But as the project continues and you incrementally collect more data, problems get bigger and bigger and then at the end of the project there’s a massive problem and it’s really inefficient to go back through that data. Managing it correctly from the start is much more efficient.”
There are four main reasons to implement good data management:
Risk Management
Data security is important. Backing up data, which is a major asset for any project, is an important risk management strategy. Managing risk in relation to sensitive data, privacy issues, Intellectual Property and private industry data is also important.
Transparency
Transparency is about protecting yourself. Some climate scientists, for example, have had to deal with people suggesting that they’re making up their work, that it’s a big conspiracy. Having all your data readily accessible and discoverable ensures transparency and defends you again unfounded accusations.
Exposure
Studies now show that researchers who make their data open get more exposure and get more citations.
Mandate
It’s becoming more of a mandate by funders like WAMSI and peer reviewed journals are requiring data to be made publicly accessible.
Data management at WAMSI
In terms of the workflow, when the WAMSI project is finished or almost complete, that data must be deposited either in the Pawsey Data Portal or the CSIRO or AIMS data centre. Once that’s done and the metadata is finalised there’s an 18 month embargo period. So once data has been deposited it gives the researcher time to write up papers for publishing before that data is then made public.
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| WAMSI data management workflow |
“So it’s all about how do I discover this data and how do I access this data,” Mr Edwards said. “The idea is to create metadata, which feed into the national infrastructure so you should eventually be able to do a Google search for the ‘Kimberly WAMSI data’ and then Google should come up with the website where the data can be accessed.
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| Pawsey data portal page for WA Node Ocean Data Network |
How is it being used?
From the raw data there is good functionality through the Pawsey data portal that researchers can use. Some researchers are already using it for collaboration with restricted access.
Big data analytics enable us to find new cures and better understand and predict the spread of diseases. Police forces use big data to catch criminals and even predict criminal activity and credit card companies use big data analytics it to detect fraudulent transactions. A number of cities are even using big data analytics with the aim of turning themselves into Smart Cities, where a bus would know to wait for a delayed train and where traffic signals predict traffic volumes and operate to minimize jams.
Why is it so important?
The biggest reason big data is important to everyone is that it’s a trend that’s only going to grow.
As the tools to collect and analyze the data become less and less expensive and more and more accessible, we will develop more and more uses for it.
And, if you live in the modern world, it’s not something you can escape.
For researchers, being FAIR (Findable, Accessible, Interoperable and Reusable) will ensure it doesn’t go to waste.
This article is based on a presentation given by Luke Edwards at the 2015 WAMSI Research Conference
The good-news El Niño story for Western Australia’s oceans
By Jaci Brown, Madeleine Cahill, Ming Feng and Xuebin Zhang, CSIRO The Conversation.
While eastern Australia trembles at the impending El Niño this year, potentially increasing heat waves and bushfires, the coastal waters of Western Australia (WA) would find El Niño a welcome relief from the heat.
In the summer of 2010-11 WA’s oceans were struck by devastating marine heatwaves, with temperatures rising up to 5C above average, causing mass deaths of marine life and coral bleaching.
Temperatures have remained warm since, due to the lingering effects of the large 2010-11 La Niña. But El Niño could be the relief these waters need for marine life to recover.
Why is the water so warm?
The water temperature off the WA coast is determined largely by the Leeuwin Current, which flows south along the WA coast from Indonesia. The Leeuwin Current is unique in the world as it is the only subtropical poleward-flowing boundary current on the eastern side of an ocean basin.
Most coastal currents, such as the East Australian Current and the Gulf Stream, are found on the western side of ocean basins.
The Leeuwin Current occurs because of the “gap” between Australia and Indonesia that connects the Pacific and Indian Oceans. The easterly winds over the Pacific Ocean pile warm water up on the western side of the ocean basin. This increases the sea level through the Indonesian archipelago. The high sea level signal is then transferred down the coast of WA, creating pressure gradients that draw in warm water and push it southward, forming the Leeuwin Current.
The Leeuwin Current can be identified as a narrow band of warmer water adjacent to the coast. Image: CSIRO
The easterly winds over the Pacific Ocean vary over time, being stronger in La Niña years and weaker in El Niño. The changing wind strength alters the amount of water piled up in the west of the Pacific and hence the sea level near Indonesia: higher in La Niña years and lower in El Niño. The changing sea level then influences the strength of the Leeuwin Current.
La Niña drives marine heatwaves
In a La Niña year, a stronger-than-normal Leeuwin Current forms off the northwest coast and flows southward, finally wrapping into the Great Australian Bight, extending to the west coast of Tasmania. The current also means warmer-than-normal water is transported further south along the WA coast, so temperatures are higher. In an El Niño year, the current weakens, and ocean temperatures fall.
La Niña drove the 2010-2011 marine heatwave (as well as the exceptional flooding in eastern Australia). Warm water has been flowing in the Leeuwin Current since 2010 without the usual reprieve brought from El Niño events.
Sea level anomaly 2010-2015
The warm water has led to extensive coral bleaching along with flooding and damage to sea grasses. Species along the coast of southwestern Australia are used to living in cooler temperate waters, and the heat wave resulted in mass deaths for a wide range of species.
How will El Niño alter the Leeuwin Current this year?
An El Niño has been forecast for this year and the easterly winds over the Pacific ocean have weakened. As a result satellites are already detecting a lower than normal sea level signal in the western equatorial Pacific.
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| Sea level map for March 2015 from satellite data. Blue areas near Indonesia show sea levels are lower then normal. AVISO |
A typical measure of El Niño is the Nino3.4 index which measures sea surface temperatures in the Pacific Ocean. The Nino3.4 index is very strongly correlated with sea level in the western equatorial Pacific.
Sea level at Fremantle is a good indicator of the strength of the Leeuwin Current. It tends to follow the Nino3.4 index and western equatorial sea level observations but with a delay of a few months. This few month delay is the time taken for the sea level change in the western Pacific to influence the strength of the Leeuwin Current near Fremantle.
Given that an El Niño has been forecast for 2015 and the sea level is dropping in the western Pacific, it seems very likely that we will see a weakening in the Leeuwin Current and cooler water temperatures along the coast of WA.
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| Timeseries of Nino3.4 (a measure of the El Niño and La Niña variability) compared to sea level in the western tropical Pacific and sea level at Freemantle (a measure of the strength of the Leeuwin current) |
Jaci Brown is Senior Research Scientist at CSIRO.
Madeleine Cahill is Oceanographer at CSIRO.
Ming Feng is Principal research scientist, Oceans and Atmosphere Flagship at CSIRO and WAMSI.
Xuebin Zhang is Senior Research scientist, Sea level rise at CSIRO.
This article was originally published on The Conversation.
Video: Understanding ENSO
This Bureau of Meteorology video explains what El Niño–Southern Oscillation (ENSO) is, how the cycle works including the science behind the phases, and the potential impacts on Australia’s climate and weather.
Kimberley box jellyfish may be first found in deep water
By Emily Piesse (ABC)
A school of box jellyfish found off the Kimberley coast in Western Australia may be the first of the species to be recorded in deep water.
Scientists discovered the jellyfish in March during a biodiversity survey in Camden Sound, about 200 kilometres north of Derby.
“We did a 1,500-metre video tow and counted 64 of these large box jellyfish, and they were all located within about half a metre of the seabed,” CSIRO principal research scientist John Keesing said.
The jellyfish were found 42 metres below the ocean’s surface, close to a reef, which is unusual for the animal.
“As far as we know it’s the first time that’s been found,” Dr Keesing said.
“These animals are ones we normally associate with coastal beaches and mangrove creeks, so certainly much closer to the mainland than we had found them [this time].”
He said it was unclear why the jellyfish were at a great depth.
“It’s possible that being close to the seabed, that they are able to actually avoid some of the stronger tidal currents,” Dr Keesing said.
Scientists from the CSIRO, Australian Institute of Marine Science and the Western Australian Museum were involved in the survey, as part of a study for the Western Australian Marine Science Institution.
Links:
Keesing J, Strzelecki J, Stowar M, Wakeford M, Miller K, Gershwin L, Liu G (Feb 2016) Abundant box jellyfish, Chironex sp. (Cnidaria: Cubozoa: Chirodropidae), discovered at depths of over 50 m on western Australian coastal reefs Scientific Reports doi:10.1038/srep22290
The $30 million Kimberley Marine Research Program is funded through major investment supported by $12 million from the Western Australian government co-invested by the WAMSI partners and supported by the Traditional Owners of the Kimberley.
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Kimberley reef life considered on microscopic level
Written by Natasha Prokop (SNWA)
Using cutting-edge genomic analyses researchers are investigating how the Kimberley marine environment’s unique conditions affect organism movement in the region.
CSIRO researcher Dr Oliver Berry says the Kimberley’s massive 10m-plus tidal ranges and complex geography are likely to produce unique dispersal patterns.
These movement patterns influence the inter-dependence (connectivity) between reef populations.
“The movements of water in the Kimberley are amazingly complex and powerful,” Dr Berry says.
“But does this mean that populations are well-mixed? Or does it mean that they are very insular because the tides and currents disrupt movements?”
“By the end of the year we hope to have an answer.”
Dr Berry says defining the degree of connectivity in the region will help identify the appropriate scale for management.
But he says despite the Kimberley’s high biodiversity and distinctiveness this is the first dedicated genetic study on marine connectivity.
The ongoing study has involved collecting more than 5,000 minute tissue biopsies of important organisms from the upper Dampier Peninsula and Buccaneer Archipelago for genetic analysis.
“We sampled species that have a spectrum of types of life histories that will expose them in different ways to the currents,” Dr Berry says.
The researchers targeted seven ‘focal species’ including the coral reef damselfish (Pomacentrus milleri), harvested molluscs (Trochus niloticus), coral (Acropora aspera), harvested fish (Lutjanus carponotatus) and seagrass (Thalassia hemprichii and Halophila ovalis) for their importance as habitat-formers or harvested species.
The movements of marine organisms, which affects connectivity amongst reefs and regions, happens mostly at larval life stages during which time larvae are transported by tides and currents.
But researchers can’t put tags or transmitters on microscopic larvae to track their movements, so they must infer this from the genetic relationships between populations.
Dr Berry says this genetic analysis poses its own challenges.
“In the marine environment, historically it has been difficult for genetics to resolve relationships between populations,” he says.
Therefore they used cutting-edge genomic techniques that have only recently been adopted by ecologists.
The scientists plans to use thousands of single sequence polymorphisms or SNPs (“snips”), which are regions of DNA where a single nucleotide differs in a sequence.
For example, ‘AGTTA’ might be a version of a gene carried by one individual, while another might carry ‘ACTTA.’ These variations act like ‘tags’ for the movements of organisms.
The benefit of using SNPs is the large number of markers that can be used, which should give researchers the ability to detect subtle patterns of connectivity.
Notes:
This project relates to themes 2 and 3 of the Kimberley Science and Conservation Strategy.
Study co-investigators include James Gilmour, Kathryn McMahon, Glenn Moore, Zoe Richards, Mike Travers and Jim Underwood.
The project was undertaken with the assistance and support of the Bardi Jawi rangers and traditional owners and Mayala traditional owners whose local knowledge was invaluable to the fieldwork component.
The $30 million Kimberley Marine Research Program is funded through major investment supported by $12 million from the Western Australian government co-invested by the WAMSI partners and supported by the Traditional Owners of the Kimberley.
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Science for restoring and enhancing estuary values – Vasse Wonnerup
Report from the National Estuaries Network Science Forum on Barrier Estuaries
The Department of Water, Water Science Branch and Busselton office together with Geocatch, hosted the National Estuaries Network Science Forum on Barrier Estuaries with special focus on the Vasse Wonnerup System (VWWS) – a wetland of international significance (Ramsar, 1990).
Around 60 estuary managers, researchers and interested community members met in Busselton to exchange information about the Vasse Strategy, science needs for estuary management and the current state of the VWWS.
Opening comments highlighted that aligned and collaborative sciences, supported by robust baseline level data are essential for effective decision-making.
Implementing the Vasse Strategy includes a restructure of governance arrangements, development of a business case to fund the strategy, reviewing the drainage infrastructure and continued catchment management interventions.
The history of flow and drainage modifications designed to protect Busselton from flooding were also shown to have contributed to the eutrophic conditions in the lower rivers and estuaries.
Advances in hydrological modelling and smarter engineering solutions are being investigated to achieve essential flood protection as well as better water quality by increased dilution of lowland river flows, helping to reduce nutrient concentrations and the undesirable expression of nuisance algal blooms and fish kills.
Early stage research projects, part of the South West Catchment Council Research Node for the Vasse Wonnerup Wetlands will explore quantitative food web structure, nutrient sources and sinks and socio-economic factors.
The connection with and potential impacts on the receiving water body – Geographe Bay were also explored. Geographe Bay has one of the largest seagrass meadows on the WA coast. A nation-wide risk assessment for seagrass meadows indicated that climate-driven temperature increase poses the greatest threat to South West seagrass integrity and that this is a greater threat than estuarine water nutrient discharge to Geographe Bay due to the drying climate pattern.
The feedback from members of the National Estuaries Network was that all of the elements needed for successful restoration appear to be in place but the integrated and thoughtful synthesis of all actions, progress and estuary health status updates would greatly assist communication between all stakeholders and sustain the momentum of support that has emerged.
Community interest is high, there has been 18 years of GeoCatch activity in catchment restoration and some highly visible media campaigns for behaviour change such as “Save the Crabs and Eat Them”. Community members appreciated the opportunity to engage with estuary managers and researchers.
Vasse Wonnerup System and adjacent Geographe Bay are incredible natural assets; with the strong community interest, there are opportunities to greatly enhance eco-tourism activities around this wetland benefiting the economy, society and environment.
We thank all the people who participated in this event. The Abstract booklet includes the speakers and their contact information.
National Estuaries Science Forum on Barrier Estuaries (Busselton)
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What’s eating you? Solving the seagrass mystery
Written by Cristy Burne
THE waters of the Bardi Jawi Indigenous Protection Area (IPA), 160km north of Broome, are paradise for seagrass: warm water, lots of light and a pristine, protected environment means these seagrasses grow fast, so why are they so short?
The answer, according to CSIRO marine ecologist Dr Mat Vanderklift, could change the way we think about healthy seagrass systems.
“The dictum in seagrass ecology is that seagrass is mostly not eaten, but that’s perhaps just a modern phenomenon,” he says.
“Most of what we know about seagrass comes from places that have been heavily fished and hunted for centuries, but if we look at places with pretty intact food webs, places like the Kimberley, it seems that seagrass is eaten a lot.”
Working with the Bardi Jawi Rangers, Dr Vanderklift is part of an ongoing collaborative project to learn more about ecological processes in the Kimberley.
“We’re currently focused on understanding how much seagrass is being eaten, and what’s eating it,” he says.
The team’s 2014 work indicates part of the answer lies with the rabbitfish (Siganus lineatus) or barrbal, a food source important to local communities.
The initial clues, he says, came from the mouth morphology and gut contents of a single fish.
Subsequent analysis of 30 barrbal caught in three places around islands in the Bardi Jawi IPA indicated “half to three-quarters of what’s in their stomach is seagrass,” Dr Vanderklift says.
Recently the team have turned their attention to green turtles (Chelonia mydas) or goorlil, tagging the herbivores to study how often and when they use seagrass beds.
“When we’re out there on the boat, we can see as the tide’s rising, these turtles are moving out across the seagrass beds,” he says.
“A logical inference is that they’re coming in to eat the seagrasses.”
Dr Vanderklift says he is excited by what the team has already achieved and will continue to learn.
“The rangers have a wealth of experience and knowledge about the system, and combining that knowledge with some of the approaches we are taking in as scientists is really profitable,” he says.
Established in 2006, the Bardi Jawi Rangers are facilitated by the Kimberley Land Council and manage more than 250km of coastline and 340,700 hectares of land, 95,000ha of it is Bardi Jawi IPA.
“I get to spend time and interact with these guys and learn from them,” Dr Vanderklift says.
“They teach me a lot, they know a lot.”
Notes:
This story pertains to deliveries in themes 1 and 2 of the Kimberley Science and Conservation Strategy.
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What do you value about the Kimberley coast?
Murdoch University is gathering information on what local residents value about the Kimberley coast and waters and what preferences you have for its management. The WAMSI research project aims to assist Government to make informed decisions about coastal management, now and into the future.
We want to hear from as many different people as possible through our online survey. Every voice counts! Just click on the link:
http://www.landscapemap2.org/kimberley
The survey will take around 30 minutes and all information you give will be anonymous. There is also a small thank you gift once you finish the survey but these are limited so get in quick.
Please help us out and have your say about how you would like to see the Kimberley coast managed in the future!
Contact Jennifer Strickland-Munro (J.Strickland-Munro@murdoch.edu.au) if you would like any more information on the study.
Read more:
Kimberley Marine Science Program survey to quiz residents about favourite coastal spots.
What is the Kimberley worth?
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Kimberley Traditional Owners establish research agreement with WAMSI
The first of several legal research agreements between the Western Australian Marine Science Institution (WAMSI) and Traditional Owners of the Kimberley has been signed paving the way for a consistent and respectful partnership approach to conducting marine science in the region.
The opportunity to develop a standard for conducting research projects within the Kimberley was welcomed by Traditional Owner groups who have had concerns about the way engagement and research has been approached previously in many circumstances.
“The Dambimangari Traditional Owners wanted to establish formal guidelines to oversee work in their land and sea country to make sure it is approached respectfully and properly,” Dambimangari Aboriginal Corporation CEO Peter McCumstie said. “This agreement gives us confidence to engage more readily, providing the opportunity to share knowledge between researchers and Traditional Owners and a solid framework for future research. From this point on we don’t have to spend a lot of time on the legalities and administrative arrangements in each case, which allows us to focus on our shared goals and outcomes desired by scientists and Traditional Owners alike.“
The agreement, that will govern research in Dambimangari Sea Country, ensures that consistent steps are in place for project planning and consent, ranger and Traditional Owner involvement in fieldwork, management of intellectual property and publishing around sensitive information.
The agreement encourages the Dambimangari people to assist researchers in current projects and also to work with them to identify and partner on future research.
The Dambimangari rangers, established by Dambimangari Aboriginal Corporation to look after land and sea country, are already working with WAMSI researchers on a number of projects.
The Dambimangari Determination Area is situated north of Derby and stretches east to the Prince Regent area, covering more than 1.4 million hectares. The marine areas or ‘sea country’ encompass the tropical waters of the Lalang-garram /Camden Sound Marine Park, an important nursery area for humpback whales. It includes Montgomery Reef, Australia’s largest inshore reef, and is where culturally important sea turtle, dugong and saltwater fish can be found.
The research completed by WAMSI and the Dambimangari people will help inform the future adaptation of the Lalang-garram / Camden Sound Marine Park management plan.
“This is an important step forward in developing a solid working relationship with the custodians of the Kimberley coastline where WAMSI is undertaking 25 research projects funded by the WA government to support the marine initiatives in the Kimberley Science and Conservation Strategy,” WAMSI CEO Patrick Seares said.
“The agreement signed by the Dambimangari Aboriginal Corporation covers nine projects and is the first to be approved in the region. We’re now working through agreements with the Bardi Jawi community and the Kimberley Land Council to develop the same sort of consistent approach to conducting research in the area.
“It’s hoped that these agreements can be relied on to support future research along the Kimberley coastline making it easier and more efficient for both Traditional Owners and researchers to engage and get out on the water together,” Mr Seares said.
The $30 million Kimberley Marine Research Program is funded through major investment supported by $12 million from the Western Australian government co-invested by the WAMSI partners and supported by the Traditional Owners of the Kimberley.
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