Showcase Tag: Oceanography

From Megabytes to Megafauna: Driving Whale Conservation to New Depths with High Performance Computing

“I think whales are kind of like dinosaurs,” says Tim Frasier. “Almost everyone is interested in them at some point in their childhood, but some of us don’t grow out of it.”

Frasier, now a biology professor at Saint Mary’s University in Halifax, Nova Scotia, is following his dream. His lab studies genetic variations in whale populations to fuel conservation efforts using high performance computing (HPC). Their present focus is on the North Atlantic right whale and Saint-Lawrence beluga.

By observing the variability of an individual’s genome over its lifetime, Frasier and his students determine how inbreeding and traumatic events, such as ship strikes or entanglement in fishing gear, make individuals and populations less able to recover and reproduce.

The Frasier Lab sequences whale genomes from minuscule pieces of skin collected humanely by field teams. They then compare the variation in gene expression in healthy and injured whales, the life histories of which they know thanks to data collected by researchers through photo-identification over the last several decades. All these data provide the basis to understand how the cumulative effects of inbreeding and multiple stress factors can cause individuals to not reproduce or live as long.

Frasier specifies, however, that these analyses involve millions of DNA fragments, which take up huge amounts of both storage space and computing power. “You just can’t do it on a normal computer.” Access to ACENET and the Alliance’s supercomputing facilities are instrumental in enabling his lab to tackle complex genetic analyses that would otherwise be impossible.

Frasier gets asked a lot how this kind of information translates into helping conservation. One way is by influencing policy. Existing legislation imposes limits on different industries according to their impact on whales. For example, a North American right whale hit by a ship or entangled in a fishery somewhere along the east coast of the US and Canada could trigger either a ship slowdown in the area or completely shut down that fishery for the season. He explains that these triggers might only be quantified based on whether the whale died or not, “like a yes-no question.” But if Frasier’s research can show that these incidents change their reproductive success for years afterward, then it would also demonstrate that current measures are vastly insufficient to help populations recover and thrive in the long term.

Frasier’s work both advances our understanding of whales and provides a framework for devising more appropriate measures to encourage population recovery. It also highlights the importance of computing resources in modern biology research and conservation. “Without ACENET, we wouldn’t be able to do this work,” he says. “It’s just such a great resource that we have, and many of the geneticists in Canada that I know feel that way.”

Deciphering the Role of the Invisible Marine Life

In terms of impact and sheer numbers, microbes dominate our planet. The tiny single-celled organisms invisible to the naked eye live everywhere on Earth – in the atmosphere, the earth’s crust and in our own bodies. The world’s oceans are also teeming with microbes – accounting for more than 90% of the ocean biomass. For Julie LaRoche, microbes represent an important indicator of the effects of climate change on ocean life. LaRoche is a biology professor and ocean scientist at Dalhousie University and the Canada Research Chair in Marine Microbial Genomics and Biogeochemistry. “We study how phytoplankton and marine bacteria are affected by increases in temperature and decreases in pH, changes that are both linked to the increase of carbon dioxide in the atmosphere. Marine microbes are key players in marine biogeochemical cycles or, simply put, they are key players in the recycling of nutrients and other elements in the ocean. Changes in the balance of the recycling will affect the productivity of the ocean, including the higher trophic life – fish and other sea creatures.” Instead of microscopes, LaRoche uses genomics and next generation sequencing techniques to study the diversity and function of ocean microbes. She says the technology has represented a huge leap forward for the science of microbiology. It has led to many discoveries of new taxonomic groups and biochemical pathways in marine microbes since its development a decade ago. LaRoche and her team have obtained the genomic sequences of microbes they have collected on ocean expeditions around the world and close to home in places such as the Bedford Basin and the Scotian Shelf. The sequences are entered into a huge database where they are analysed in the context of other oceanographic observations. As the observations accumulate over several years, the initial sequence information will serve as reference in the study the long term effects of climate change on life on Earth. “While we are discovering the roles of the microbes that live in the North West Atlantic waters, we are also establishing a baseline for comparing with the observations obtained in future studies, and assess what changes have taken place in the microbial population as a result of climate change.” Studying microbes means dealing with huge numbers. First, there are approximately 5 x 1030 microbial cells on earth representing an estimated 100 million species. The database that LaRoche and her team are working with is also huge; some 20 million sequences to date with four to five million pieces in each data set. “These are big files that take up a lot of memory. We can’t do it on a normal computer so we have to use ACENET.” LaRoche and her team have already compiled and analysed three and a half years of data using the ACENET system. The work is enabling scientists to understand the ways the world’s oceans – and life on Earth – are changing. “As the oceans continue to warm and to become more acidic, the microbial life within it may migrate closer to the poles in response,” she says. “This may affect the entire biome of the sea and that is why we need to study it.”

Predicting the Influence of the Ocean on Machines and Structures

Understanding how machines and structures perform in the ocean has important implications for everything from the way ships manoeuvre to how tidal power turbines respond to massive hydraulic forces. One University of New Brunswick scientist is working hard to increase that understanding and he’s employing some powerful computational tools. Andrew Gerber is a professor of mechanical engineering at UNB. He’s an expert in the field of computational fluid dynamics (CFD) and high performance computing, a discipline that focuses on solving the equations that govern fluid movement using supercomputers. Supercomputers are needed to study in detail how ocean turbulent fluid motion interacts with machines and structures situated within it. Oceans are extremely demanding environments. For man-made systems to survive requires detailed understanding, something that supercomputer simulations can provide. Gerber is involved with a number of important projects including a tidal power study in the Bay of Fundy and a project with Defence Research and Development Canada to study the performance of Canadian naval submarines. “We do a lot of work with submarines,” says Gerber. “We simulate extreme manoeuvres on the computer to see what’s happening to the forces and moments acting on the body of the submarine as it moves through the water. It’s very expensive for the navy to do experiments of this type so our simulations allow them to make predictions without the need for extensive experimentation”. Gerber’s work with tidal power focuses on making detailed fluid flow predictions to support tidal power turbine deployments in the Bay of Fundy. He and his colleagues at UNB are working with the Fundy Ocean Research Centre for Energy (FORCE), and with researchers at Acadia University and Dalhousie University, to measure tidal flow and energy potential in the Minas Passage near Parrsboro and in Grand Passage at Brier Island, Nova Scotia. This work will have a huge impact on where turbine arrays are deployed considering issues such as survivability and maximizing power output. The tidal study involves huge volumes of water requiring complex calculations. Twice each day 10 cubic kilometers of seawater are forced through the Minas Passage – 10 billion tons of water that represent an outflow more than 40 times the amount that flows from the Saint Lawrence River over the same period of time. With technical support from ACENET and funding from the Canada Foundation for Innovation, Gerber set up a “contributed system,” a computer cluster operated by Gerber’s UNB laboratory and managed by ACENET. Under the system, any unused cycles are turned over to ACENET for other researchers to use. The system is powered by the latest Graphical Processing Unit (GPU) hardware, and combined with a CFD simulation software (EXN/Aero) that can efficiently utilize the new hardware, the complex tidal simulations can be completed much more rapidly with high-resolution. In addition to his work at UNB, Gerber is also a partner in a spinoff company called Envenio Inc., a Fredericton-based firm that provides computational fluid mechanics services and engineering software development to engineers and companies. Its flagship product is EXN/Aero, which is specifically designed for next generation hardware. Gerber says that as climate change becomes more prevalent, understanding the movements of fluids in the oceans and atmosphere and their impact on infrastructure will become crucial. “One of the goals of Envenio is to help engineers build better designs for extreme weather events in the ocean or atmosphere and to provide the computational tools to do so.”

Acadia Professor Uses ACENET to Unlock Tidal Power Secrets

In Richard Karsten’s office at Acadia University the entire Bay of Fundy has been reduced to a grid made up of 100,000 triangles displayed on an oversized computer screen. The data points – tide height, current, water depth – have been carefully plotted by the mathematics professor and his graduate students to create a computer model that can pinpoint the nature of the tide at any spot on the bay, at any given second for the next 25 years. It’s a staggering amount of data. “At the basic level, what we’re studying is how fast the water is flowing at any given point,” he says. “Then we get into more detail and look at things like the variations in the direction and speed of flow.” The 270 kilometre-long bay Karsten is studying is one of the most unique places on Earth; a submerged rift valley where the world’s highest tides reach a daily height of 16 meters, moving 160 billion tonnes of seawater in the process and powering a dynamic ecosystem teaming with life. It’s a place often mentioned in the same breath as the Great Barrier Reef and the Amazon; where a dozen species of whales regularly congregate and millions of shore birds gather every year to fatten themselves up for their migration to South America. It could also be North America’s next great source of hydroelectric power. A number of projects are underway to harness those powerful tides. Most notable is the Fundy Ocean Research Centre for Energy or FORCE, a government and industry supported test centre for in-stream tidal energy located in Parrsboro, Nova Scotia. There are smaller projects as well, including one by Fundy Tidal Inc., a corporation headquartered on Brier Island Nova Scotia. Fundy Tidal is working with partner Clean Current Power Systems Inc. of British Columbia to develop five small community tidal projects to sell energy through Nova Scotia’s Community Feed-In Tariff (COMFIT) program. Karsten’s research, along with information provided by project partners Dalhousie University, the University of New Brunswick and Dynamic Systems Analysis, will provide information for those projects by locating the spots where engineers can best place underwater turbines, along with long term projections of just how profitable those turbines will be. “Numerical models are relatively cheap as opposed to testing,” he says. It is one reason his research has attracted funding support from Natural Resources Canada, the Offshore Energy and Research Association of Nova Scotia and NSERC. Charting terabytes of information presents a significant “big data” problem, but Karsten has a valuable tool in his arsenal – a computer network hundreds of times more powerful than the computer on his desk. By tapping into the ACENET system that links large computers located in a number of Atlantic Canadian universities, he has access to a super computer network capable of, in aggregate, computations of up to 68 Teraflops. “What would take years on a desktop takes us a few days or weeks with the ACENET supercomputer,” he says. The speed of the system allows him to run various “what if” scenarios, such as adding more turbines to a particular location or seeing what additional forces would be generated by a storm surge. “It means we are able to answer questions quickly.” Hydrographers have been maintaining accurate tidal charts for more than a century, but until recently no one was too concerned with information like flow direction and force – information that is vitally important to tidal power engineers. If, for example, the water doesn’t flow back and forth along the same direction with each tide, a turbine might have to be turned constantly to face the flow – a design feature that would increase the cost of the operation significantly. Karsten’s research provides critical support to the development of a tidal energy industry both in Nova Scotia and nationally. Such an industry would produce substantial amounts of sustainable, renewable electricity that would reduce Nova Scotia production of greenhouse gases and decrease its dependency on foreign fuels. Last year, some of his research activities included making extractable power estimates for all major Nova Scotia tidal resources. In total, the calculations estimated that the tidal resource could support over 1400 MW of installed capacity with only a minor impact on the tides. This is 55% of Nova Scotia generation capacity. “Tides are ultimately predictable,” says Karsten. “That’s what makes them so appealing as an energy source. But there are a lot of variables – rocks or seaweed on the bottom, deep channels or shoals within a passage – that affect the energy in the tidal currents.” There is a less pragmatic purpose for Karsten’s research as well. As biologists and oceanographers at Acadia and other universities scramble to unravel the delicate ecosystem of the Bay of Fundy, they are sharing data in an attempt to understand how tides affect the movements of fish and other sea life. “You would think we know a lot about Fundy but we really don’t yet,” he says. “It’s still very much a mysterious place.”