Acadia University

In Search of Apple Perfection

Zoë Migicovsky has the secret sauce to help farmers get more fruitful crops. The assistant professor of biology at Acadia University and Canada Research Chair (Tier II) in Agri-Food and Sustainable Agriculture works her magic by combining genetic data from fruit crops and agriculturally important trait information about the plants and then analyzing the data so plant breeders can make predictions about what their plants will produce in terms of fruit.

“Agriculturally important traits would be things such as when an apple might ripen or what its aroma might be,” Migicovsky says. “With an apple seedling, you’re going to be waiting four to seven years for there to be enough fruit for you to have a meaningful evaluation of what that fruit is like.”

There’s an enormous resource investment in that seedling in terms of breeding the plants, fertilizing, watering, managing for pests and disease and pruning, to name a few. “Then at the end, most of the plants won’t have desirable traits,” Migicovsky says. “That will be true regardless, but if we can make predictions about some of those traits early on, we can reduce the number of plants that need to be culled at a later date and narrow down which are more likely to be desirable plants later on.

She sums up the problem she’s addressing by quoting from an October 23, 2023 Financial Times article in which a breeder started with 90,000 trees. Of those, “Only 357 varieties made it to a second round of trials, 18 went to a third and 13 reached the final round.” The article states that apples are like diamonds in that way.

In order to do her work, Migicovsky needs computational resources that will handle large genomic trait datasets and link them together. “The plant breeder isn’t going to screen for 200,000 genetic markers. They would like to only screen for a couple, so we need to know which ones are the best for them to do that. If you have a quarter of a million columns to compute, you’re not going to do that on your laptop,” Migicovsky says. “We need computational resources like those available through ACENET and the Digital Research Alliance of Canada.”

The more genomic data she has, the more likely she is to find good predictors, but the more genetic data she has, the more computational resources she also needs.

Using ACENET resources saves her money in her research budget and enables continuity in her work. It’s a shared system, so her students are able to access her lab’s files and software. “It’s helpful because students are only there for a relatively short time so this allows for one student to pick up where another left off.”

The Secrets of Birds

Anyone who has watched a flock of birds fly by knows that keeping track of individual birds can be complicated. But what if you had to chart the movements of a whole population of birds using data taken over many years and using different measuring tools and data sources? That’s precisely the challenge that one Acadia biology professor and his graduate student had to tackle. Dr. Mark Mallory and Master’s student Christine Anderson have been studying the migratory movements of herring gulls based on electronic data, and they are using the ACENET computer network to help them with their work. Anderson is using tracking data from a herring gull population in Nunavut and comparing them to other data from places such as the Great Lakes, Brier Island, Sable Island and Newfoundland to find out how each population is behaving differently from the others. It’s a complicated process because the data comes in many forms. Some of it comes from a process called Doppler triangulation that pinpoints the birds’ movements in a range of 350 metres to one kilometre. Other data takes the form of GPS tracking – an accuracy of just a few metres. “With the ACENET system I can input data with different errors and the system will take each error into account and give me an accurate reading,” says Anderson. “It can take up to two weeks to run a program. It’s something I couldn’t possibly do on my laptop.” Mallory says that Anderson is the first of his students to make use of the ACENET system. He says her study has some important practical components that go beyond pure scientific understanding. “First of all, by understanding their movements over time it allows us to identify places where we need to create protected areas for migrating birds. Also, it allows us to understand what these birds do to their environment and how they interact with humans. Are they spending more time over a landfill or over water? Are they creating a danger around airports? Are they picking up diseases like avian influenza that can infect humans? These are important questions.” Anderson says that she doesn’t have a lot of background in computers, but the support she received from ACENET was invaluable. “The ACENET staff are incredibly helpful,” she says. “I couldn’t have done this project without them.”

Mining William Blake

If he were alive today William Blake would have been a multimedia artist, says Acadia University English professor Jon Saklofske. After all, the great British poet and visual artist left a complex and vast body of work ranging from the romantic to the surreal. “Blake was an inventor,” says Saklofske. “He would have realized that computers are important tools and I think he would have made good use of them.” Saklofske certainly is making good use of the technology. He is an active participant in the emerging field of digital humanities – the practice of applying computer technology in various ways to the study of the humanities. He’s using it for his ongoing research into the works of Blake, but he’s gone much further than that, creating a digital online tool called NewRadial that helps scholars conduct and share online research. “People have been digitizing works of literature and art like crazy for the last 15 years,” says Saklofske. “Now it’s time for us to start doing something with these vast digital collections.” Saklofske’s interest in online research began when he started using the William Blake Archive, a web-based multimedia source featuring the works of Blake. “It’s a great site, but there are limitations,” he says. “The interface didn’t allow me to do everything I wanted to do.” He began working on an alternative interface, a modified way of accessing and participating in the Blake Archive – one that would allow more detailed search parameters and user participation. He dubbed the online platform “NewRadial” and immediately extended it beyond the study of Blake to work with other online multimedia collections. NewRadial has proved to be a huge boon to Saklofske’s research. For example, he’s used it to study Blake’s artistic representations of the Biblical Leviathan. “Blake drew Leviathan as a coiled serpent,” he says. “NewRadial allows me to collect other representations of Leviathan during Blake’s time and compare them with Blake’s work.” The platform also promotes open social scholarship as other researchers are able to create their own collections, leave marginal comments or start a comment stream. “By integrating diverse and often isolated online resources through something like NewRadial, we can look at 500 years of written culture and understand how the way we tell stories, use language and express our worldview has changed and evolved over the centuries. It’s a very effective tool.” By getting involved with ACENET, Saklofske was able to move NewRadial off of the small Macintosh server that it originally resided on and make it faster and more powerful. ACENET also opened his eyes to new possibilities for the technology and for the field of digital humanities. Digital humanities is a broad field and one that a lot of traditional humanities scholars still have a hard time taking to, according to Saklofske. “There is still a noticeable divide between computer science and the arts. A lot of the time the efforts of Compute Canada tend to be directed toward science, but there is really a lot that can be done in the study of the arts as well. Computers are changing the way we do research and communicate that research with each other and a broader public. William Blake was very much about thinking beyond the box, in the same way that computers are allowing us to think beyond the page.”

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.”