Wednesday, April 21, 2021

Federal government launches national quantum strategy

The glass exterior of the Institute for Quantum Computing.

This article originally appeared on the Institute for Quantum Computing website.

The University of Waterloo’s Institute for Quantum Computing welcomes the federal budget commitment to investing in a national quantum strategy.

Alongside industry partners and other Canadian universities, the University of Waterloo has been advocating for a national quantum strategy to maintain Canada’s competitive edge as we develop and commercialize tomorrow’s technological breakthroughs, and train the workforce needed to bring these discoveries to market.

The government has shown its willingness to invest in innovative areas where Canada plays a leadership role. Canada was one of the first to prioritize quantum research, which has positioned us well to lead in this emergent technology.

“We are grateful for the federal government’s ongoing support and commitment toward this important strategy,” said Charmaine Dean, vice-president, research & international at the University of Waterloo.

“Canada was an early leader in foundational quantum science and technology development, and while collectively this country continues to punch above its weight ranking behind only the United States and China in quantum computing IP, this strategy will help retain Canada’s first-mover advantage in the field.” 

IQC was established nearly 20 years ago to bring together scientists, mathematicians, and engineers to advance fundamental and applied research on quantum technologies. Through the development of quantum communications, computing, materials and sensor applications, the work done at IQC is instrumental in transforming some of the world’s largest industries and driving future economies.

The many companies that have spun out of IQC include Quantum Benchmark, an error-correcting software for quantum-computing hardware, and QEYnet, which is developing satellite-based quantum key distribution.

To learn more about how the research at the University of Waterloo harnesses the quantum laws of nature to develop powerful new technologies and drive future economies, visit the IQC website.

Using machine learning to develop personalized cancer treatment

Ming Li (L) is a University Professor at the Cheriton School of Computer Science and the Canada Research Chair in Bioinformatics. Hieu Tran (R) is an Adjunct Assistant Professor at the Cheriton School of Computer Science and Senior Research Scientist at Bioinformatics Solutions, a Waterloo-based company that uses machine learning to sequence and identify proteins.

Ming Li (L) is a University Professor at the Cheriton School of Computer Science and the Canada Research Chair in Bioinformatics. Hieu Tran (R) is an Adjunct Assistant Professor at the Cheriton School of Computer Science and Senior Research Scientist at Bioinformatics Solutions, a Waterloo-based company that uses machine learning to sequence and identify proteins.

Researchers at the Cheriton School of Computer Science have applied machine learning to identify tumour-specific antigens, which could help make personalized cancer vaccines practically feasible and more accurate.

In cancer, when a missense mutation occurs in a cell’s DNA, a single nucleotide substitution in the DNA results in a different amino acid in the peptide the cell produces, explains Hieu Tran, an Adjunct Assistant Professor at the Cheriton School of Computer Science. “The peptide that has the changed amino acid is recognized by our immune system as foreign, even though it is synthesized by cancer cells from our own body.”

This mutated peptide is known as a neoantigen — an antigen that’s present only on the surface of cancer cells, Hieu Tran explained. “If we can figure out what the neoantigens are on cancer cells, they can be used to develop a cancer vaccine — a vaccine that’s personalized to the cancer patient and which uses the patient’s own immune system to attack the tumour.”

“When a cell becomes cancerous the human leukocyte antigen or HLA system knows about it,” adds Ming Li, a University Professor at the Cheriton School of Computer Science, who also holds the Canada Research Chair in Bioinformatics. “The HLA system presents peptides on the surface of cells. If the HLA system presents a normal peptide on a cell’s surface, the T cells of our immune system know that it is a self-peptide and they don’t attack it. The T cells attack only the cells with mutated peptides, the ones with neoantigens on their surface.”

The trick, however, is finding these tumour-specific neoantigens — essentially a needle in a large haystack. Not surprisingly, it is a bewilderingly difficult task to do using conventional methods, but it is crucially important when developing a personalized cancer vaccine.

Amino acids are the building blocks of peptides and ultimately protein molecules. By convention, amino acids are labelled using a one-letter code. For example, the amino acid alanine is labelled A, arginine is labelled R, asparagine is labelled N, and so on. A peptide’s amino acid sequence can be considered as a word of composed of these letters.

“If you are familiar with natural language processing, you’ve likely seen your mobile phone guess the next word you might have typed as you compose a message. You write ‘how’ and it suggests ‘are’ and if you type ‘are’ it suggests ‘you’,” Hieu Tran said.

“We applied a similar machine-learning model to determine the amino acid sequence of neoantigens based on this one-letter amino acid code. If I know your immunopeptidome — the thousands of short 8 to 12 amino acid peptide antigens displayed on the cell surface — and I know that a neoantigen is different from your existing peptides by just one mutation, I can train a machine learning model using your normal peptides to predict the mutated peptides. We used a recurrent neural network — a machine learning model we call DeepNovo — to predict the amino acid sequence of neoantigens.”

To do this the researchers downloaded the immunopeptidome datasets of five patients with melanoma, a type of skin cancer, which they then used to train, validate and test their machine learning model.

“Our machine-learning model expanded the predicted immunopeptidomes of those patients by 5 to 15 percent,” Hieu Tran said. “We also discovered neoantigens, including those with validated T-cell responses that had not been reported in previous studies.”

Even more impressively, the machine learning model is able to personalize the results — that is, it identifies specific neoantigens for each individual patient.

“Cancer immunotherapy is quickly becoming a fourth modality of cancer treatment, alongside surgery, chemotherapy and radiotherapy,” adds University Professor Li. “Every patient is different and every cancer is different, so cancer treatment shouldn’t be the same for all. Treatment should be tailored to the patient, and that’s what our personalized machine learning model allows us to do.”

New Community of Practice for continuous improvement and change management

People sit around a conference table.

A message from Human Resources.

The Office of the Associate Provost, Human Resources is excited to announce the successful launch of a University wide Continuous Improvement (CI) and Change Management (CM) Community of Practice. To further develop institutional CI/CM expertise, the CoP aims to provide a supportive space for those seeking to learn more about CI and CM or, those who are already working on similar initiatives. 

Hosted on March 31, 2021, the inaugural session was attended by 60 members and focused on the principles of CI and CM and showcased the benefits of an integrated model. Improving the communities learning roadmap, our members also helped to identify suitable topics for future meetings and knowledge-sharing networks.

“The CoP is an awesome opportunity to learn from talented people across the campus community. I am really looking forward to learning more about continuous improvement and change management tools and resources. Hearing stories from others across campus is really thought provoking and provides inspiration for new ways of tackling big challenges in my own work,” writes Amanda Annarilli, manager, operations, Student Success Office.

Get involved, become a CI&CM CoP member today. We invite members of our University community to join the growing CoP. Together we can expand our institutional expertise and shape the future of CI and CM at Waterloo.

Questions? Please contact Raghda Sabry, HR project manager, or Samantha Murray, change management advisor.

Participate in GreenHouse's first Health Challenges Forum

Health Challenges Forum banner featuring a healthcare worker wearing PPE.

The GreenHouse social impact incubator at St. Paul’s University College in collaboration with Concept at the University of Waterloo will be hosting its first Health Challenges Forum on Tuesday, May 18, 2021 from 2:00 to 4:30 p.m.

This free virtual event will explore the most pressing challenges faced by healthcare professionals at local acute care, long term care, and home care medical organizations.

Interested in joining the forum? We’re looking for students and researchers to join the discussion with speakers from Grand River Hospital, Schlegel Villages, and the Local Health Integration Network. The goal is to discuss problems of various themes under all three sectors to gain a better understanding of why these challenges exist, who is impacted and how. 

Register by May 9, 2021 to learn more about the issues that exist within healthcare, create new research collaborations and begin developing solutions.

Wednesday's notes

"Due to a recent Workday update, employees registering for Organizational and Human Development’s current workshops may notice Workday lists the delivery mode as in-person even though they have been set-up as instructor-led webinars," says a note from Organizational and Human Development (OHD). "A few employees have contacted us with questions about the matter. Rest assured that our workshops continue to be held online using Microsoft Teams and not in-person. It appears this error is occurring with scheduled workshops that require a specific date/time unlike self-led webinars which have open access with no date or time limitations."  

"The wording error has been brought to Workday’s attention so hopefully the next update will reflect the actual method of delivery. If you have any questions about our current spring workshop offerings, please contact for clarification and assistance."

Yesterday, former Minneapolis Police officer Derek Chauvin was found guilty of murder and manslaughter in the May 2020 death of George Floyd. Though justice was done in this instance, the University recognizes that elements brought out in the trial, and the ongoing issue of anti-Black racism, may have an effect on members of our University community.

If you or anyone you know are in need of support, below are resources, including mental health supports, available to members of the University:

Link of the day

National Canadian Film Day

When and Where to get support

Students can visit the Student Success Office online for supports including academic development, international student resources, leadership development, exchange and study abroad, and opportunities to get involved.

Instructors can visit the Keep Learning website to get support on adapting their teaching and learning plans for an online environment.

Course templates are available within your course in LEARN to help you build and edit your content and assignment pages quickly.

The following workshops, webinars, and events are offered by the KL team (CTE, CEL, ITMS, LIB):

Employees can access resources to help them work remotely, including managing University records and privacy of personal information. Here are some tips for staying healthy while working from home.

Stay informed about COVID cases on campus by consulting the COVID case tracker.

Whether you’re a student or faculty member, the Writing and Communication Centre has virtual services and programs to help you with all of your academic writing needs. This term we have added evening and weekend one-to-one appointments with our peer tutors, and our NEW one-to-one workshops, where you can learn the content directly from one of our writing advisors.

  • Undergraduates: Work with us to brainstorm, draft, revise, and polish your assignments in one-to-one appointments. Ask questions and learn writing tips at our Instagram Live Q&A sessions, and beat isolation while improving your writing skills at the weekly PJ-friendly writing groups.
  • Graduates: Meet with our advisors in one-to-one appointments. Join the online writing community at the Virtual Writing Cafés, learn how to present your work at Speak Like a Scholar, or get moving on your dissertation at Dissertation Boot Camp.
  • Faculty and Instructors: Request custom workshops for your courses, join the Waterloo writing community at the Virtual Writing Cafés, or make progress on your article, book, or chapter in one-to-one meetings with our faculty specialist.

Co-op students can get help finding a job and find supports to successfully work remotely, develop new skills, access wellness and career information, and contact a co-op or career advisor.

The Centre for Career Action assists undergraduates, graduate students, postdocs, staff, faculty, and alumni through navigating career services that are right for them. You can attend a one-on-one appointment or same day drop-in session at the CCA for assistance with cover letter writing, career planning and much more. You can also book an appointment online or visit our Live Chat to connect with our Client Support Team. The CCA is here to help you.

If you feel overwhelmed or anxious and need to talk to somebody, please contact the University’s Campus Wellness services, either Health Services or  Counselling Services. You can also contact the University's Centre for Mental Health Research and TreatmentGood2Talk is a post-secondary student helpline available to all students.

The Library has published a resource guide on how to avoid information overload.

The Faculty Association of the University of Waterloo (FAUW) continues to advocate for its members. Check out the FAUW blog for more information.

The University of Waterloo Staff Association (UWSA) continues to advocate for its members. Check out the UWSA blog for more information.

The Indigenous Initiatives Office is a central hub that provides guidance, support, and resources to all Indigenous and non-Indigenous campus community members and oversees the university Indigenization strategy.

The Waterloo Indigenous Student Centre, based at St. Paul’s University College, provides support and resources for Indigenous students, and educational outreach programs for the broader community, including lectures, and events.

WUSA supports for students:

Peer support (Visit to book an appointment):

  • MATES – Available Monday to Friday, 10:30 a.m. to 9:30 p.m.; Saturday and Sunday, 10:30 a.m. to 5:30 p.m. (online only)
    • Support sessions available in the following languages: Cantonese, English, Hindi, Mandarin, Portuguese, Punjabi, Spanish, and Urdu.
  • Glow Centre – Available Monday to Friday,  4:00 p.m. to 8:00 p.m. (online only)
  • RAISE – Available Monday to Friday – Varied hours (online only)
  • Women’s Centre – Available Monday to Friday, 2:00 p.m. to 5:00 p.m. (online only)

Bike Centre – Will be reopening soon

Campus Response Team, ICSN, Off Campus Community and Co-op Connection all available online. Check for more details.

Food Support Service food hampers are currently available from the Turnkey Desk on weekdays from 7:30 a.m. to 7:00 p.m. in the Student Life Centre. If you have any questions please email us at

Centre for Academic Policy Support - CAPS is here to assist Waterloo undergraduates throughout their experience in navigating academic policy in the instances of filing petitions, grievances and appeals. Please contact them at caps@wusa.caMore information is available.

WUSA Commissioners who can help in a variety of areas that students may be experiencing during this time:

WUSA Student Legal Protection Program - Seeking legal counsel can be intimidating, especially if it’s your first time facing a legal issue. The legal assistance helpline provides quick access to legal advice in any area of law, including criminal. Just call 1-833-202-4571

Empower Me is a confidential mental health and wellness service that connects students with qualified counsellors 24/7. They can be reached at 1-833-628-5589.

When and Where (but mostly when)

Healthy Warriors at Home (Online Fitness)

Drop-in to Warrior Virtual Study Halls on Wednesdays from 5:30 p.m. to 7:00 p.m. Come together in this virtual space to set goals and work independently or in groups each week.

Livestream Exercises for Waterloo staff: Join us for an energy boosting Bootcamp or a fast and effective Express Home Workout. Open to UW Staff and subsidized by the Staff Excellence Fund.

Renison English Language Institute continues to offer virtual events and workshops to help students practice their English language skills.

Warriors vs. Laurier Blood Donation Battle. Join your fellow Warriors, donate blood and help us win the Blood Battle against Laurier for a second year in a row. Set up a profile or add the PFL code: UNIV960995 to your account if you have a account already. Questions? Contact

Portfolio & Project Management Community of Practice (PPM CoP) session, "Equity, Diversity and Inclusion (EDI) in Project Planning" Wednesday, April 21, 9:00 a.m. to 10:00 a.m. Register for this event.

Retirement of Steve Furino, Thursday, April 22, 3:30 p.m., Microsoft Teams.

A Year of COVID-19: Disparities, Inequities, and Inequalities, the first in a three-part series, Friday, April 23, 1:00 p.m. to 3:00 p.m. Please register to receive a link to this online event.

Waterloo Philosophy Sharma Lecture: "Deepfakes, Deep Harms" presented by Regina Rini, Canada Research Chair in Philosophy of Moral and Social Cognition at York University, Friday, April 23 from 3:30 p.m. to 5:00 p.m. via WebEx.

Lectures in Catholic Experience presents Progressive or Conservative? Archbishop Pocock and the Renewal of the Church in Canada featuring Peter Meehan, St. Jerome's University's President and Vice Chancellor, April 23, 7:30 p.m. online.

NEW - Women in Computer Science, Responding to Everyday Bias: How to Recognize it and Interrupt it, Monday, April 26, 12 noon. All are welcome to attend, but registration is required.

NEW - Bibliometrics and Research Impact Community Conference, Tuesday, April 27 to Thursday, April 29, 11:00 a.m. to 4:30 p.m. Register for this online event.

Positions available

On this week's list from the human resources department, viewable on the UWaterloo Talent Acquisition System (iCIMS):

  • Job ID# 2021-6470 - Administrative Coordinator - School of Planning, USG 5
  • Job ID# 2021-6459  Administrative Officer - School of Architecture, USG 12
  • Job ID# 2021-6410 - Director, Campus Wellness - Campus Wellness, USG 19
  • Job ID# 2021-6472 - Event and External Relations Coordinator - School of Planning, USG 6
  • Job ID# 2021-6493 - Grants and Contracts Manager - Institutional Research - Office of Research, USG 9 – 11
  • Job ID# 2021-6372 - Library Clerk: Resource Sharing – Library, USG 4
  • Job ID# 2021-6488 - Program Administrator – OHD, USG 6
  • Job ID# 2021-6379 - Records Coordinator - Office of the Registrar, USG 5 – 7
  • Job ID# 2021-6321 - Director of Economics and Resiliency - Dean of Environment Office, USG 13
  • Job ID# 2021-6337 - Director, Climate Resilient Infrastructure - Dean of Environment Office, USG 13

Secondments/Internal temporary opportunities

  • Job ID# 2021-6349 - Accommodation Consultant, Mental Health - AccessAbility Services, USG 8
  • Job ID# 2021-6360 - Director, CEE Business Services - Co-operative and Experiential Education, USG 16
  • Job ID# 2021-6414 - HR Data Systems Specialist - Human Resources, USG 9
  • Job ID# 2021-6425 - International Recruitment Specialist - Marketing & Undergraduate Recruitment, USG 9
  • Job ID# 2021-6476 - Librarian, Special Collections & Archives – Library, USG 9 – 11
  • Job ID# 2021-6388 - Undergraduate Recruitment Specialist - Office of the Registrar, Marketing & Undergraduate Recruitment, USG 8