Cycling

Shifting gears: How data science led Madeleine Bonsma-Fisher from studying germ models to bike lanes

Christopher.Sorensen — Tue, 09 May 2023 20:03:34 +0000

Shifting gears: How data science led Madeleine Bonsma-Fisher from studying germ models to bike lanes

Christopher.Sorensen Tue, 05/09/2023 - 16:03

Cutline

Madeleine Bonsma-Fisher, a post-doctoral researcher at U of T's Data Sciences Institute, is studying traffic "stress" in Toronto in order to pinpoint where more cycling infrastructure is needed (photo by Johnny Guatto)

Adina Bresge

Topic

Our Community

Cycling

Data Sciences Institute

Institutional Strategic Initiatives

Cities

Faculty of Applied Science & Engineering

Faculty of Arts & Science

Physics

Research & Innovation

When Madeleine Bonsma-Fisher bikes through Toronto, she sees where her research meets the road.

Each street she pedals down presents as a series of data points: She’ll count 15 people weaving past one another on the sidewalk, while three cars cruise down a road that takes up 80 per cent of the space.

A cycling activist, Bonsma-Fisher is studying traffic patterns as part of her post-doctoral research at the University of Toronto’s Data Sciences Institute, an institutional strategic initiative that is a tri-campus hub for number crunchers across disciplines. Before that, she modelled evolutionary interactions between microbes.

The common thread? Data and data analysis.

“I don't want to say that data science is the answer to everything, but I am finding that there is so much you can do,” Bonsma-Fisher says. “It gave me a lot of freedom to really just do whatever I wanted.”

Her current research focuses on what might seem like a simple question: At any point in Toronto, can you cycle to essential destinations – grocery stores, health care and schools – within 30 minutes, using only bike lanes and traffic-calmed roads?

The answer, she says, is far from straightforward. It requires sophisticated data analysis to make a map of the entire city and rate each road according to traffic stress, which accounts for factors such as traffic volume, speed limits and physical separation.

The next step, Bonsma-Fisher says, is to pinpoint places where infrastructure could improve access to cycling as a comfortable and convenient mode of transportation, such as dedicated bike lanes and physical separation from car traffic.

As she searches for active transportation solutions, Bonsma-Fisher is working with two advisers at the Data Sciences Institute: Shoshanna Saxe, an associate professor in the department of civil and mineral engineering, and Timothy Chan, a professor of mechanical and industrial engineering – both in the Faculty of Applied Science & Engineering.

“What’s cool about the Data Sciences Institute is that the vision is to bring people together with different experience and allow people to make that jump to a different field.”

The winding road of Bonsma-Fisher’s research career – and the data focus that underpins it – began when she arrived at U of T’s School of Graduate Studies in 2014 with a physics degree and an interest in using the field’s principles to solve biological problems.

Her supervisor, Sidhartha Goyal, an associate professor in the department of physics in the Faculty of Arts & Science, suggested she look into CRISPR – a term she hadn’t heard before, but one that would become the subject of both her master’s and doctoral studies.

You may have heard of CRISPR in the context of genome editing, but the technology is derived from a bacterial defence mechanism that is analogous to adaptive immunity in humans. Many bacteria have an immune system called CRISPR that allows them to store memories of viruses in their own DNA – like a genetic gallery of viral “mug shots,” Bonsma-Fisher explains.

As part of her PhD research, Bonsma-Fisher built a simple mathematical model to explore how computer-simulated interactions between populations of bacteria and viruses shape CRISPR immune memories.

The paper, published in the journal eLife earlier this year, provides fresh insight into the evolutionary “arms race” between viruses and bacteria – with viruses mutating to evade immune recognition, while CRISPR builds bacteria’s DNA database of previous attackers. The simplicity of the model helped narrow down the most prominent processes in a complicated system, Bonsma-Fisher says.

Down the road, Bonsma-Fisher says the model could contribute to our understanding of immunity in more complex organisms, including humans.

“Some of the conclusions we think are going to apply to any type of immune system-virus interaction.”

While she was chipping away at her microbial models, Bonsma-Fisher made another discovery: data analysis skills were in short supply – and high demand – among her fellow graduate students. So, she co-founded the U of T Coders group to give researchers across all disciplines a chance to learn the basics of programming and teach each other new techniques through hands-on, member-led tutorials.

“A lot of people would try to learn by themselves,” she says, “and there would be a lot of struggle and tears. U of T coders was a place for people to support each other through all of that.”

Bonsma-Fisher is interviewed by CBC about cycling infrastructure in Ottawa.

Bonsma-Fisher’s turn toward sustainability-oriented research around cycling came naturally.

Like many university students, Bonsma-Fisher relied on her bike to commute to campus and was all too familiar with the challenges of being a cyclist in a car-focused Canadian city.

Upon moving to Ottawa, Bonsma-Fisher joined the board of advocacy group Bike Ottawa, where she contributed data analysis to report on how the COVID-19 crisis has influenced cycling trends and advocated for a bike-share program.

The more she learned about transportation infrastructure, the faster the wheels in her head began to turn. What if she could combine her passions – cycling and data analysis – to make the streets safer and cities more sustainable?

“It felt like there were these two parts of me,” she says. “I [used data analysis] to bring together a lot of things I care about: environmental sustainability and having a more human-scale place to live.”

Saxe, who is Canada Research Chair in Sustainable Infrastructure, says Bonsma-Fisher’s personal investment in the subject is foundational to her work. “I find people do better research when they are intrinsically motivated by the topic,” she says.

Bonsma-Fisher notes that quantitative data alone can’t solve every problem, particularly when it comes to questions of equity and people’s lived experiences. Nevertheless, she says surveys suggest that most adults would be willing to bike if they were physically protected from cars – and data can help point policymakers to the places where infrastructure is needed most.

“I know from my experience what I want to bike on and what it feels to be on a road that feels unsafe,” she says. “If the city wants to get people biking – and they do – they need to make it safe.”

Good for you, better for the planet: U of T cyclists pedal toward a more sustainable future

Christopher.Sorensen — Thu, 20 Oct 2022 20:13:42 +0000

Good for you, better for the planet: U of T cyclists pedal toward a more sustainable future

Christopher.Sorensen Thu, 10/20/2022 - 16:13

Cutline

Beth Austerberry, executive director of Bikechain, helps Walid Maraqa, a grad student in biostatistics, perform basic maintenance on his bike (photo by Geoffrey Vendeville)

Mariam Matti

Topic

City & Culture

Climate Positive Energy

Cycling

Institutional Strategic Initiatives

Cell and Systems Biology

Faculty of Applied Science & Engineering

Faculty of Art & Science

One of Ayush Sharma’s first stops upon moving to Canada to attend the University of Toronto was Bikechain on the George campus.

An international student from Delhi, Sharma says he had barely been in Toronto a week before visiting the educational bike repair space for students.

“I enjoyed cycling back home in India and I wasn’t sure how to go about doing it in Toronto,” says Sharma, who is completing a major in biodiversity and conservation biology and a minor in geographic information systems. “It’s a big city and it seems a little intimidating – and bikes are expensive.

“I wasn’t really sure where to start.”

Bikechain proved to be a great landing pad. The non-profit organization, which has been around since 2005, not only offers free workshops on how to fix a flat tire, do-it-yourself bike repairs and free bike rentals to students – it’s part of a supportive and growing local cycling community in and around campus.

“People come here on a basic level to fix their bike,” says Beth Austerberry, executive director of Bikechain. “A lot of people also come here because they want to learn.”

Bikechain is a non-profit on the St. George campus that offers free workshops on how to fix a flat tire, do-it-yourself bike repairs and free bike rentals to students (photo by Geoffrey Vendeville)

While Toronto is often criticized for its car-focused infrastructure, there’s no denying the rapidly growing popularity of cycling as a healthy, sustainable mode of transportation – a future that U of T is actively supporting through research, infrastructure and community building efforts.

On the St. George campus alone, there are 36 Bike Share Toronto stations – part of a larger, city-wide network of 680 stations and 7,185 rental bikes (U of T Scarborough also has a Bike Share station near the bus loop on Military Trail). There are also bike lanes that run through the campus along University Avenue, College Street, St. George Street, Wellesley Street, Bloor Street, Hoskin Avenue and Harbord Street, among others.

U of T is also adding hundreds of new above-ground and below-ground spaces to park your bike as part of as part of the Landmark Project, which will transform the historic heart of the St. George campus into a greener, more pedestrian friendly space on top of a massive underground geoexchange system that will significantly reduce campus emissions.

At U of T Scarborough, cycling admittedly requires a bit more planning than it does on the St. George campus – but there are enviable upsides, too.

Hanno Rein, an associate professor in the department of physical and environmental sciences at U of T Scarborough, says he discovered a particularly scenic cycling route to campus that he felt compelled to share via a blog post.

“The nice thing about it is that there are no cars around, so the entire trip is all trails,” he says. “I wanted to encourage others to commute by bike, even if it is in Scarborough.”

Rein, who also teaches in the David A. Dunlap department of astronomy and astrophysics and the department of physics on the St. George campus, says he loves cycling because of the environmental and health factors.

“It’s very enjoyable,” he said. “It’s the nicest commute I can think of.”

However, he’s also quick to point out that infrastructure for cyclists could be better and safer.

Many U of T students, staff, faculty and librarians treat cycling as a year-round activity in Toronto (photo by Daria Perevezentsev)

At U of T Mississauga, BikeShare offers 48-hour bicycle, helmet and lock rentals to U of T Mississauga students free of charge. Located in the Student Centre extension, BikeShare has commuter-style bikes and mountain bikes for rent and is open until the end of October. The program also offers educational repairs similar to Bikechain, providing tools for basic fixups.

Cyclists at U of T Mississauga also have access to the 3.4-kilometre Nature Trail Loop along Credit River and nearby Erindale Park offers a scenic route for cyclists and mountain bikers in the area. Meanwhile, the City of Mississauga is considering the implementing a system similar to Bike Share Toronto to expand transportation options. The system would include stations with bikes, e-bikes and e-scooters.

Southern Ontario’s snowy winters can pose a challenge to bicycle commuters on all three campuses – though many are increasingly treating it as a year-round activity.

Tony Harris

Tony Harris, a professor in the department of cell and systems biology in the Faculty of Arts & Science, says he appreciates being available to avoid traffic on his commute and likes that he’s reducing his environmental footprint by not driving.

His approach to slush and snow?

“I think it’s really important to find good routes that are safe,” he says, adding that it takes him about 30 minutes to bike to the St. George campus from his home. “In the winter, you have to be more cautious about slippery conditions.”

A long-time cycling commuter, Harris adds that he’s perfected the art of cycling during a Toronto winter.

“I wear my normal clothes and then my fleece and I have a yellow cycling jacket on top,” he described. “I wear two pairs of gloves and that really helps my hands. I have an inner glove that’s a running-type glove and then I wear a fleece glove over top. I also wear a toque underneath my helmet. “One other thing is long underwear.

“Having two layers everywhere seems to be the key.”

His advice to students who are new to cycling? Map out your routes.

“Before you head out, find where the dedicated cycling lanes are. If there aren’t dedicated cycling lanes, find one-way side streets that allow you to avoid the busier streets and cars,” he says.

U of T researchers are also playing a key role in helping to map out the university’s transportation future with sustainability – and cycling – in mind.

Marianne Hatzopoulou

Marianne Hatzopoulou, a professor in the department of civil and mineral engineering in the Faculty of Arts & Science, belongs to a research team that’s trying to understand how U of T commuters’ habits and other personal choices contribute to greenhouse gas emissions.

The project, funded by the Climate Positive Energy research initiative, will launch a travel survey in January to collect data from students, staff, faculty, and librarians to understand how they commute to campus every day.

“The second part of the project is to quantify the carbon footprint of commuting and the greenhouse gasses associated with commuting to U of T to measure what our footprint is from transportation,” explained Hatzopoulou.

“The third element is to run some experiments to understand what would make people switch their mode of transportation, especially those who are driving.”

Hatzopoulou’s team wants to understand where there are opportunities to promote more sustainable and active modes of transportation and where the challenges lie.

“There’s a lot of research out there that actually quantifies the benefits of cycling as a mode of transportation,” she says.

As for Sharma, riding his bike around campus not only introduced him to the city, it saved him precious time traveling between classes on the St. George campus – not to mention lowering his carbon footprint.

Most importantly, he says, it has helped him find a community through Bikechain, where he is now a co-president and runs workshops.

“There is a mix of undergraduate, graduate, PhD students as well as faculty and non-U of T students,” he says of the group. “Bike shops in general can be dominated by cis males and it can be an unwelcoming space for other people, but Bikchain has always been an inclusive and open space for everyone.

“That’s one of the main reasons I’ve stuck with the community for so long.”