UQ-Bio introduces undergraduates to quantitative biology

Candid photo of postdoctoral researcher Luis Aguilera seated at his desk with computer showing microscope images and programming code.
Luis Aguilera, a postdoctoral researcher in the Department of Chemical and Biological Engineering

For a decade and a half, the annual Q-Bio Conference has been accompanied by a summer school to train early-career scientists in the techniques of quantitative biology, or “q-bio.” Now, this unique program has been expanded to help undergraduates get their start in the field thanks to an innovative instructional reboot developed by CSU postdoctoral researcher Luis Aguilera and others.

“Past offerings were designed mostly for participants from big labs who had existing experience in coding and quantitative biology. When we decided to offer an undergraduate version of the program, we wanted to broaden access so that anyone could engage in this fascinating discipline,” said organizer Brian Munsky, associate professor of Chemical and Biological Engineering, whose NSF CAREER award supports the Undergraduate Quantitative Biology (UQ-Bio) Summer School.

He credited Aguilera’s team of Engineering and Natural Sciences colleagues with “completely transforming the program to create a far more equitable learning environment.”

Fast-forwarding the biosciences

Biomedical research can produce staggeringly large amounts of data from many different sources, and any given experimental question might require years of conventional research before a breakthrough.

Quantitative biology applies modern mathematical, statistical, and computational methods to beat these odds, enabling researchers to develop predictive models and simulations of biological systems. With these tools, they can more quickly gain insight into cellular processes, weed out less-promising hypotheses, and design better experiments. The techniques have the power to rapidly advance our fundamental understanding of diseases and cellular biology, and to reduce development costs for new medicines and therapies.

Given the power of q-bio tools and techniques, and the promise they hold for impacting human health, it’s no wonder that the skill set is in high demand.

“The field still lacks enough trained professionals,” Aguilera said. “A quantitative biologist needs to have a deep understanding of the biomedical process, and strong computational skills. Scientists with both skill sets are rare.”

Innovative instruction

With this in mind, Aguilera and his peers set out to give interested undergraduate students a path into quantitative biology. The result, known as UQ-Bio Summer School, combines coding tutorials, technical seminars, and career discussion panels.

Participants work with real examples of super-resolution microscopy images. They learn to extract data from these image and video sources and then perform statistical analysis, machine learning, and simulation tasks to understand the data they’ve harvested.

They practice applying these new skills in group exercises, and see how these techniques are used in real-world case studies during seminars presented by invited speakers. Participants also attend special career mentoring discussions with senior scientists and academics to discuss the opportunities and challenges associated with advancing within the q-bio fields.

It’s a holistic introduction to the challenging and rapidly growing field of quantitative biology – an opportunity that arose in part during the coronavirus pandemic.

A screenshot from a UQ-Bio session on particle tracking shows images and Python code
A screenshot from a UQ-Bio lesson shows how interactive programming code and instructional content coexist on the page.

“Travel restrictions forced us to rethink new ways to design the UQ-bio program using technological tools,” Aguilera said. That includes such tools as Github for code distribution, Slack for communication, and Dropbox and Google Drive for file sharing.

Programming workshops, in particular, were an instructional pain point.

“Teaching scientific programming to 35 in-person and +100 online students is very challenging. Imagine if one line of code doesn’t work for one of the students. That is enough to stop the flow of the whole class,” said Aguilera.

The team conducted programming workshops using Google Colab, which allowed them to package lessons as web pages with Python programming code blocks embedded in the instructional content. Each user can edit and execute the code in place, in their own web browser, without any installation or configuration hang-ups.

The result strikes a balance between the efficiency of group instruction, and the experiential power of hands-on learning.

Aguilera’s team decided to continue using these adaptations because they were such a hit with students and teachers in the fully virtual 2021 event. Even better, the new delivery methods made it possible to make the 2022 program a hybrid event and reach students who were unable to attend in person.

The overall effect has been to bring more young students in contact with the skills and potential of quantitative biology than ever before.

“In the past, when the program was meant for graduate students, we had at most one or two undergraduates per year,” said Munsky. “This year, we had 30 in-person students and 187 registered online.”

Outdoor group photo of UQ-Bio participants shows a couple dozen people in two rows beneath a flowering tree on the CSU campus.
Participants in the 2022 UQ-Bio Summer School pose for a group photo on the CSU campus.
The UQ-Bio Summer School and q-bio conference were supported by NSF CAREER Award (Division of Molecular and Cellular Biology); Office of the Vice President for Research; Walter Scott, Jr. College of Engineering; College of Natural Sciences; College of Veterinary Medicine and Biomedical Sciences; the Department of Microbiology, Immunology and Pathology; and the Flint Animal Cancer Center.