Graduate students in biological sciences attend computation bootcamp

As biology increasingly transforms into a discipline driven by ever-expanding datasets and computational analysis, students need new forms of training to follow best practices and build a successful research career. With a new award from the National Science Foundation, the University of Chicago Biological Sciences Division will test an innovative curriculum, which it piloted at the Marine Biological Laboratory, that focuses on hands-on learning in computational methods and how to use these tools in a rigorous and reproducible way.

For a week before their first courses begin, incoming graduate students from every BSD graduate program will travel to Marine Biological Laboratory in Woods Hole, Mass. for a weeklong “bootcamp” session. This training experience—combined with a responsible research course taught later in the academic year—will prepare students with the programming, statistics and documentation practices needed to produce cutting-edge science.

After two years of developing and piloting the bootcamp, known as QBio, co-directors Victoria Prince, Stephanie Palmer and Stefano Allesina received an award from the NSF Innovations in Graduate Education Program to evaluate this unique approach and share it with other institutions. The goals reflect prevailing trends in biology towards more data-heavy research, they said.

“More than ever, biology is a quantitative discipline, and no matter what kind of biology you do, you need the same kinds of quantitative skills to model and analyze your data,” said Palmer, assistant professor of organismal biology and anatomy at UChicago. “Our students really need to be completely conversant in these methods, and they're better prepared for academia and for the broader workforce when they have those skills.”

“We are very pleased that this pilot program at MBL, which addresses a clear need in advancing biological education, will expand into the curriculum at UChicago and potentially at other institutions with the support of this grant,” said Melina Hale, co-director of the MBL, vice provost for academic Initiatives and the William Rainey Harper Professor in the Department of Organismal Biology and Anatomy at UChicago.

Beginning with the 2015 incoming class, new BSD students journeyed to MBL for an immersive week learning key concepts such as writing code, exploring and visualizing data, scientific statistics, and analyzing images and video. A combination of tutorials and hands-on workshops using real data, taught by BSD faculty, gave students a foundation in the methods they’ll later apply to their own research.

Additionally, the experience provided a chance for students to meet each other across disciplinary boundaries and practice teamwork with their new colleagues.

“One of the other big goals of the proposal is to really teach people how to work in teams,” said Prince, professor of organismal biology and anatomy and dean and director of BSD Graduate Affairs at UChicago. “Because we've done the bootcamp twice already, we're building on knowledge that we already have, and we're already seeing changes in the way the students interact with one another.”

Starting this academic year, all first-year students will subsequently take a redesigned ethics course that refreshes skills learned during the bootcamp alongside traditional discussion-based learning about ethical research practices. The technical instruction provides practical guidance for conducting rigorous and reproducible experiments, through standards such as documenting and sharing programming code used for data analysis.


“Part of ethical research conduct is that you are using the right tool, that you make it available for other people to use, that other people can understand what you did, how you did it, and when you did it, with which data, and if they do it on their own data, will it give them the same result,” said Allesina, professor of ecology and evolution and a member of the Computation Institute. “Otherwise, we're not really doing good science.”


Locating the bootcamp at MBL also provides several benefits for the new students. Outside of coursework, students hear talks about MBL research and take a trip on MBL’s “Gemma” collections boat to collect specimens from the Atlantic Ocean.


“We want our students to see MBL as part of our campus, and learn about opportunities for collaborative research,” Palmer said. “MBL has a special atmosphere and it shows the students this other part of the UChicago experience.”


As part of the IGE program, the co-directors will evaluate the impact of the curriculum on the next three classes of incoming graduate students, with repeated assessments of how the training affected their technical skills and confidence later in their career. Besides publishing and presenting the results of these assessments, all course materials from the bootcamp and responsible research course will be available as open source on Github (you can view last year’s materials here). 


The award is part of the NSF Innovations in Graduate Education Program, which supports projects that pilot, test and validate innovative and potentially transformative ways to teach science, technology, engineering and mathematics.


“These IGE projects address important challenges in graduate education: diversity, career pathways and transferrable skillsets,” said Jim Lewis, NSF acting assistant director for Education and Human Resources. “Learning more about what constitutes effective graduate education will enable us to prepare a STEM-capable workforce that can meet the evolving demands of a fast-paced, data-intensive, globally networked world.”