Mathematical and Computational Sciences

U of T startup's technology plays role in 'critical breakthrough' in coronavirus research

geoff.vendeville — Fri, 21 Feb 2020 16:47:19 +0000

U of T startup's technology plays role in 'critical breakthrough' in coronavirus research

geoff.vendeville Fri, 02/21/2020 - 11:47

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U of T PhD candidate Ali Punjani is CEO of the startup Structura Biotechnology, which produces a tool that combines computer vision and machine learning to help researchers create 3D visualizations of proteins (photo by Ken Jones)

Geoffrey Vendeville

Topic

Breaking Research

Coronavirus

Mathematical and Computational Sciences

Artificial Intelligence

Computer Science

Entrepreneurship

Faculty of Applied Science & Engineering

Global

Innovation & Entrepreneurship

Startups

ThisIsThePlace

U of T Scarborough

Software that grew out of a ��߲ݴ�ý research project facilitated what’s being described as a “critical breakthrough” in the search for a vaccine for the novel coronavirus.

Researchers at the University of Texas at Austin and the U.S. National Institutes of Health recently announced that they have created the first 3D, atomic scale map of the part of the virus that attaches to and infects human cells – known as the spike protein. They published their work in the journal Science this week.

The researchers relied on cryoSPARC – software spun out of Ali Punjani’s PhD research in computer science at U of T and designed by alumnus Suhail Dawood – to process data of the coronavirus spike protein and obtain accurate 3D images of the spike in real time. Punjani’s startup, Stuctura Biotechnology, bills the tool as a way for academic researchers and pharmaceutical companies to rapidly recover 3D protein structures, taking some of the guesswork out of drug discovery.

“The work by UT Austin and the NIH demonstrates the power of structural biology,” Punjani said. “We can actually look at a new disease that was discovered just a couple of months ago and see how it works at the molecular level. It’s very exciting.”

The World Health Organization has declared the novel coronavirus, or COVID-19, a global public health emergency. There have been more than 76,000 confirmed cases and over 2,200 deaths to date.

Jason McLellan, an associate professor in molecular biosciences at UT Austin and one of the study’s co-authors, said cryoSPARC enabled him and his team to process data while travelling, speeding up their efforts. It took just 12 days for the researchers to go from a raw sample to producing an atomic scale map of the protein spike and submitting their manuscript to Science.

“One of their novel algorithms, referred to as 3D Variability Analysis, provided insights into the dynamic motions of the coronavirus spike protein that are important for receptor-binding and membrane fusion,” McLellan told U of T News.

Punjani co-founded Structura Biotechnology while still a PhD student in an effort to bring cryoSPARC to market. His supervisor, David Fleet, a professor in the department of computer science and U of T Scarborough's department of mathematical and computer sciences, initiated the research behind cryoSPARC and joined the startup as an expert advisor.

Student club at U of T Mississauga to connect women in STEM, promote diversity and inclusion

Christopher.Sorensen — Mon, 27 Jan 2020 15:55:14 +0000

Student club at U of T Mississauga to connect women in STEM, promote diversity and inclusion

Christopher.Sorensen Mon, 01/27/2020 - 10:55

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Members of the Women in Science and Computing club's executive committee, including Fatima Minhas (far left) and Vaneezeh Siddiqui (fifth from left), pose for a photograph at U of T Mississauga (photo courtesy of WiSC)

Blake Eligh

Topic

Our Community

Mathematical and Computational Sciences

Undergraduate Students

A new student club at U of T Mississauga is connecting women in science and computing studies with networking and career development opportunities.

Since its soft launch in December, the Women in Science and Computing club (or WiSC) has hosted three events, including an exam study session, a film screening and a career panel with a San Francisco-based leader in web development.

WiSC co-founder and president Vaneezeh Siddiqui is a second-year undergraduate student studying statistics, computer science and business at U of T Mississauga. She was attracted to the campus because of its reputation as a close-knit and diverse community with good research opportunities, but often found herself attending events on U of T’s St. George campus in an effort to connect with other female students in her field.

“I wanted to have that community here at UTM,” says Siddiqui, who founded WiSC in August 2019 by gathering a 14-member executive committee to plan networking events and outreach opportunities to connect, inspire and support its members.

“Women in Science and Computing is a place where we can talk about what we’re experiencing, find mentorship and peer support,” Siddiqui says. “The mission is to create a place where everyone, particularly female-identifying students and minorities, feel supported in their journey and don’t feel like they’re doing it alone.”

Siddiqui and Fatima Minhas, the club’s external communications director, can both recount experiences where their expertise and ambition have been disregarded by some male classmates because of their gender.

“I’ve been told – more than once – that ‘girls can’t do math,’” says Minhas, a fourth-year student studying Earth sciences and mathematics. “To be thought of as less than equal or not good enough was a shock to me, and it made me feel unwelcome.”

The women find strength in connection with other women in their fields. “You think you’re having an experience in isolation, but when you talk to other women, you see that you’re not alone,” Minhas says. “There are other women in STEM who have the same issues in industry, in the classroom and in the lab.”

Minhas says the club helps students connect outside of class and mix with peers across scientific disciplines. “WiSC unifies women in STEM on this campus,” Minhas says. “We have each other, but how do we further that relationship through professional events, networking events and bonding events?”

With start-up funding from the U of T Mississauga Students’ Union, WiSC launched its first event in January. The club hosted a career event with an all-female panel of engineers, product managers and technical leaders working with San Francisco-based tech giant Yelp. The session covered career paths, challenges and opportunities for women in the industry.

WiSC will also share information about student opportunities like hackathons, conferences and scholarships and help match students with others who might be interested in participating.

While the club is meant to connect women in STEM, the founders are heartened to see support from male classmates who are also attending events, incuding the group’s official launch in early January that featured a screening of “Dream Girl,” a documentary about women and entrepreneurship.

“Our events are open to all genders because we want to raise awareness about diversity and inclusion in STEM,” Minhas says. “Those are the types of conversations that we want everyone to be a part of so they’re aware that problems exist, but they also know how to approach a solution and be allies for their female peers.”

“It’s exciting,” says Siddiqui. “That conversation was not happening at UTM, but now it is. We can help ensure that current and incoming students in computer science feel supported.”

WiSC is planning a range of events over the Winter semester. On Jan. 31, WiSC will cohost the Citigroup Recruiting Visit career event in partnership with U of T Mississauga’s Mathematical and Computational Science Society. To commemorate the International Day of Women and Girls in Science on Feb. 11, the club is planning a fireside student chat about imposter syndrome and what it’s like to be a female student in STEM. In March, the group will host a panel of female faculty members to discuss academic career development.

For award-winning Andrew Petersen, teaching computer science is all about the 'human element'

noreen.rasbach — Wed, 20 Nov 2019 15:01:21 +0000

For award-winning Andrew Petersen, teaching computer science is all about the 'human element'

noreen.rasbach Wed, 11/20/2019 - 10:01

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“It’s easy to forget, when you’re dealing with machines, who is on the other side,” says U of T Mississauga's Andrew Petersen. “Code has to rest with real people" (photo by Drew Lesiuczok)

Blake Eligh

Topic

Our Community

Mathematical and Computational Sciences

Awards

Computer Science

Faculty of Arts & Science

Teaching

U of T Mississauga

For Andrew Petersen, teaching computer science takes a human touch.

His dedication to community and collaboration has earned Petersen a reputation as one of Ontario’s most outstanding university educators. An associate professor, teaching stream in the department of mathematical and computational sciences at the ��߲ݴ�ý Mississauga, he was recently recognized by the Ontario Confederation of University Faculty Associations (OCUFA) with the 2018-2019 OCUFA Teaching Award for his contributions to the advancement of innovation in teaching and learning practices.

“Faculty are at the heart of Ontario’s vibrant universities,” says OCUFA President Rahul Sapra, who presented the award at an October ceremony in Toronto. “Through their hard work and boundless energy, they inspire students to embrace new ideas and build a brighter future. This year’s distinguished award recipients are all dedicated and passionate teachers and mentors.”

Petersen trained to design and program computer chips, but that career took a different direction when he discovered a passion for pedagogy as a teaching assistant during his graduate studies. “I really enjoy working with students,” Petersen says.

Over the past 13 years, the first year undergraduate class has grown from 120 students to over 700, a development that has presented exciting new opportunities and challenges. “Our teaching methods and the way we interact with students has had to scale,” he says. “The personal contact with students is so important.”

That personal contact is what drives Petersen’s approach to teaching and research. “It’s easy to forget, when you’re dealing with machines, who is on the other side,” he says. “Code has to rest with real people. You’re writing code so that other people can modify it, and so they can solve a problem that a real person has. If we lose the human element, we lose focus.”

He is energized by the collaborative possibilities offered in U of T Mississauga’s new active learning classrooms. “Active learning classrooms allow us to see what students are doing,” Petersen says. “I’ve been surprised by what students get stuck on because I’ve never been able to see it firsthand before – I have a better sense now. We can do code reviews where students can see and critique each other’s code.”

That collaborative space also helps to break down barriers. “Students can see that they are making the same mistakes as other students.”

Petersen developed the Programming Course Resource System (PCRS), an open-source application for students and faculty that bundles interactive programming exercises with video and text content. “PCRS provides immediate feedback that is really important. Otherwise, students don’t know whether what they are doing is working or not,” he says. “This allows them to get immediate results.”

Data from PCRS exercises and other ongoing research helps Petersen and his colleagues to make evidence-based improvements to the curriculum. “All of my questions are driven by something that’s happening in my classes – a problem that I’m seeing, a course that needs updating or a student interaction that led me to understand something new,” he says.

Petersen also credits his tri-campus colleagues for their work to improve the student experience. “There’s a lot that co-teaching leads us to learn from each other and allows us to continually improve these courses,” he says. “When you work in a group, there’s always someone suggesting a way to do better and someone to take on that work. That’s part of what’s awesome about being here.”

“Andrew has made a huge difference, particularly in the educational research community,” says colleague Michelle Craig, an associate professor, teaching stream with the department of computer science in the Faculty of Arts & Science.

She notes that Petersen has created reading groups for students and colleagues to stay up-to-date on best practices and new pedagogical research, and also established the website for U of T’s tri-campus Computer Science Education Research Group. The site, which gathers together projects and research efforts of teaching stream computer science faculty across U of T, lists 157 publications published by group members since 2003, 102 of which were published in the past five years.

“This has changed the way we teach, and improves our practice all the time,” Craig says.

But for Petersen, the joy of his work always comes back to interactions with students.

“Classroom work is important, but much of what we do is outside the classroom – talking to students about grad school, or supporting student-led initiatives like the Cloud Developer Club,” he says. “That’s work where we can support what the students are doing and taking the next step.

“It really comes down to those interpersonal connections.”

Rescuing crops, reframing history and researching MMIW: 2019 Connaught New Researcher Award winners announced

Christopher.Sorensen — Mon, 09 Sep 2019 14:05:45 +0000

Rescuing crops, reframing history and researching MMIW: 2019 Connaught New Researcher Award winners announced

Christopher.Sorensen Mon, 09/09/2019 - 10:05

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Three of this year's 52 winners of the Connaught New Researcher Award: Eliana Gonzales-Vigil, Shauna Sweeney and Jerry Flores

Jenny Rodrigues

Topic

Our Community

Mathematical and Computational Sciences

Anthropolgy

Astronomy & Astrophysics

Awards

Biochemistry

Biology

Centre for Criminology & Sociolegal Studies

Chemistry

Computer Science

Connaught Fund

Dalla Lana School of Public Health

Earth Sciences

Economics

English

Factor-Inwentash Faculty of Social Work

Faculty of Applied Science & Engineering

Faculty of Arts & Science

Faculty of Information

Institute for Management & Innovation

Institute of Biomaterials and Biomedical Engineering

Lawrence S. Bloomberg Faculty of Nursing

Management

Mathematics

Mechanical & Industrial Engineering

Molecular Genetics

Ontario Institute for Studies in Education

Philosophy

Political Science

Psychology

Research & Innovation

Women and Gender Studies

Insects destroy up to one quarter of global crops each year, resulting in estimated losses of up to $470 billion. Even in greenhouse conditions, pests can still cause damage by making their way inside through vents.

It’s a problem the ��߲ݴ�ý’s Eliana Gonzales-Vigil aims to tackle by better understanding the complex relationship between plants and bugs.

The biological sciences researcher at U of T Scarborough is specifically looking at how to protect crops from the cabbage looper, a common pest of tomatoes and other vegetables such as peppers, cucumbers and – of course – cabbage.

“My long-term goal is to understand how plants defend themselves from insect herbivores,” Gonzales-Vigil said.

“But to achieve this, we need to understand all the players involved.”

Gonzales-Vigil is one of 52 winners of this year’s Connaught New Researcher Award, designed to help recipients establish a strong research program and increase their competitiveness for external funding. The award is part of U of T’s commitment to fostering excellence in research and innovation by supporting faculty members who are launching their academic careers.

Read the full list of Connaught New Researcher Award winners here

Up to $1 million will be distributed among this year’s winners.

“I would like to congratulate all the winners of the Connaught New Researcher Award,” said Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives.

“These researchers are doing exciting, innovative work across many different disciplines. It’s the ��߲ݴ�ý’s hope that this funding will help set the stage for world-leading scholarship and important new discoveries.”

(photo courtesy of Eliana Gonzalez-Vigil)

Gonzales-Vigil is embarking on a study to explore how impacting the gut microbiome of the cabbage looper may help tomato plants be more resistant against the insect’s attack.

“We want to test the idea of whether the microbiome of the cabbage looper is being affected by the plant’s chemistry. If yes, then can we manipulate the plant’s chemistry by adding something like a probiotic that would impede insect growth?”

She added the Connaught award will help kick-start a new line of research after having most recently focused on how poplar trees defend themselves through a waxy compound secretion.

“Having the Connaught has given me the freedom to start something that’s new,” she said, adding that she hopes her research will eventually lead to insect control methods that can be used around the world.

Shauna Sweeney

(photo by Nick Iwanyshyn)

During her undergraduate studies, U of T’s Shauna Sweeney was drawn to Caribbean history courses – in particular the history and the economy of the markets in Caribbean nations. It was an area of research Sweeney, who is herself of Jamaican background, wanted to explore further.

An assistant professor in the department of history and at the Women & Gender Studies Institute, Sweeney is currently working on a manuscript that examines the prominent role of enslaved women in developing an informal economy in the Caribbean.

She said that by selling or trading goods to each other, enslaved women asserted their own economic rights and ultimately laid the groundwork for a free community following abolition.

“In conventional studies of capitalism that consider the deeply violent and exploitative context of slavery, enslaved peoples' own economic lives and politics tend to fall out,” Sweeney said. “So, it’s important to me to restore the social and economic importance of trading to enslaved people and their descendants.”

“In addition to being commodities on paper, enslaved people actually were agents in their own economies and had economic interests of their own.”

Sweeney plans to conduct further transnational research with the Connaught award, travelling to Europe to visit the Archivo de Indias (Archives of the Indies) and the Archives Nationales d’Outre-mer (National Overseas Archives).

The research trips will also help lay a foundation for her second project, which will focus on white female slave owners.

Jerry Flores

(photo courtesy of Jerry Flores)

As a Mexican who was born and raised in Los Angeles, U of T Mississauga’s Jerry Flores brings an outsider’s perspective to a high-profile research project in Canada: an ethnography of missing and murdered Indigenous women (MMIW) and men in Toronto.

Flores, an assistant professor in the department of sociology, previously published a book about young, incarcerated Latina women.

As he heard more stories about MMIW, he began to notice similarities.

“The experiences of a lot of these women go like this: They’re abused at home by a partner or a family member and run away to get away from it,” Flores said.

“They end up on the street and participate in high risk behaviour or may end up getting involved in drugs or sex work. They meet a new partner – for young women, it’s usually an older man – that brings them home, but quickly spirals into drugs, alcohol and abuse.”

Specifically, Flores wants to study the circumstances in which Indigenous people make their way to Toronto. He’s asking: What challenges did they face to come here? Have they lost people on their journey to Toronto? What stories have they heard?

Flores is working closely with local organizations, including the Native Women’s Association of Canada and the Aboriginal Law Society in Toronto, to gather stories. Funding from the Connaught New Researcher Award will help compensate participants for their time and provide support for the community organizations that are assisting Flores in his research.

“By definition, ethnography is a study of culture. I’m trying to understand the culture of the Indigenous community in Toronto – how they negotiate life, the challenges and the high points. What is it that they need, what do they want to accomplish, and how can we as a collective – U of T Mississauga and U of T in general – support them?”

Flores hopes that the study will be able to provide concrete recommendations for policy, community action and scholarship on MMIW.

Here is the full list of winners of the 2019 Connaught New Researcher Award:

Humanities:

Tania Aguila-Way, assistant professor, department of English

Barend Beekhuizen, assistant professor, department of language studies, U of T Mississauga

Brendan de Kenessey, assistant professor, department of philosophy

Catherine Evans, assistant professor, Centre for Criminology & Sociolegal Studies

Cindy Ewing, assistant professor, department of history

Sarah Gutsche-Miller, assistant professor, Faculty of Music

Adam Hammond, assistant professor, department of English

Rosalind Hampton, assistant professor, department of social justice education, Ontario Institute For Studies in Education

Mary Elizabeth Luka, assistant professor, department of arts, culture and media, U of T Scarborough

Luther Obrock, assistant professor, department of historical studies, U of T Mississauga

Shauna Sweeney, assistant professor, department of history and Women & Gender Studies Institute

Katherine Williams, assistant professor, department of English

Life Sciences/Social Cultural

Jennifer Brooks, assistant professor, Dalla Lana School of Public Health

Aaron Conway, assistant professor, Lawrence S. Bloomberg Faculty of Nursing

Marzyeh Ghassemi, assistant professor, departments of medicine and computer science

Quinn Grundy, assistant professor, Lawrence S. Bloomberg Faculty of Nursing

Péter Molnár, assistant professor, department of biological sciences, U of T Scarborough

Olli Saarela, associate professor, Dalla Lana School of Public Health

Molecular

Michael Garton, assistant professor, Institute of Biomaterials and Biomedical Engineering

Eliana Gonzales-Vigil, assistant professor, department of biological sciences, U of T Scarborough

Thomas Hurd, assistant professor, department of molecular genetics

Hyun Kate Lee, assistant professor, department of biochemistry

Baohua Liu, assistant professor, department of biology, U of T Mississauga

Physical Science

Melissa Anderson, assistant professor, department of Earth sciences

Amy Bilton, assistant professor, department of mechanical and industrial engineering

Maryam Mehri Dehnavi, assistant professor, department of computer science

Maria Drout, assistant professor, department of astronomy and astrophysics

Murat A. Erdogdu, assistant professor, departments of computer science and statistical sciences

Tovi Grossman, assistant professor, department of computer science

Fan Long, assistant professor, department of computer science

Semechah Lui, assistant professor, department of chemical and physical sciences, U of T Mississauga

Fabio Pusateri, assistant professor, department of mathematics

Arul Shankar, assistant professor, department of mathematical and computational sciences, U of T Mississauga

Diana Valencia, assistant professor, department of physical and environmental sciences, U of T Scarborough

Stanislav Volgushev, assistant professor, department of mathematical and computational sciences, U of T Mississauga

Joseph Williams, assistant professor, department of computer science

Mark Wilson, assistant professor, department of chemistry

Social Sciences

Monica Alexander, assistant professor, departments of statistical sciences and sociology

Noel Anderson, assistant professor, political science, U of T Mississauga

Jennifer Brant, assistant professor, department of curriculum, teaching and learning, Ontario Institute for Studies in Education

Michelle Cameron, assistant professor, department of anthropology

Laura Cirelli, assistant professor, department of psychology, U of T Scarborough

Fedor Dokshin, assistant professor, department of sociology

Emine Fidan Elcioglu, assistant professor, department of sociology, U of T Scarborough

Jerry Flores, assistant professor, department of sociology, U of T Mississauga

Ethan Fosse, assistant professor, department of sociology, U of T Scarborough

Charles Martineau, assistant professor, department of management, U of T Scarborough

David Price, assistant professor, department of economics, U of T Mississauga

Tahseen Shams, assistant professor, department of sociology

Jennifer Stellar, assistant professor, department of psychology, U of T Mississauga

Jia Xue, assistant professor, Factor-Inwentash Faculty of Social Work and Faculty of Information

Marius Zoican, assistant professor, department of management and Institute for Management and Innovation, U of T Mississauga

Mathematical and Computational Sciences

U of T startup's technology plays role in 'critical breakthrough' in coronavirus research

Read more about Structura Biotechnology

Student club at U of T Mississauga to connect women in STEM, promote diversity and inclusion

For award-winning Andrew Petersen, teaching computer science is all about the 'human element'

Rescuing crops, reframing history and researching MMIW: 2019 Connaught New Researcher Award winners announced

Read the full list of Connaught New Researcher Award winners here

Shauna Sweeney

Jerry Flores

Humanities:

Life Sciences/Social Cultural

Molecular

Physical Science

Social Sciences