Educators Create Engaging Online Workshop for Integrated Biomedical Sciences Students
The COVID-19 pandemic has created an ever-changing environment requiring quick adjustment, especially in the field of research. In response to the pandemic, scientists at UK ceased non-essential research activity in the spring, and education was moved to online platforms.
While these measures were necessary to ensure safety for faculty and learners, graduate students in the University of Kentucky College of Medicine Integrated Biomedical Sciences (IBS) PhD program saw their progress interrupted. Brett Spear, PhD, professor in the department of microbiology, immunology, and molecular genetics, and former director of graduate students for the IBS program, was concerned these students would not have a way to stay occupied and engaged through the pandemic restrictions, as IBS students normally do full-time research in the summer.
“After spring break, students were no longer able to come to the lab to do research, and all their coursework moved online,” Dr. Spear said. “During the final half of the spring semester, the students could keep busy with their coursework even if they couldn’t come to lab; however, once the semester ended, there were no more courses, and they still could not do research.”
Dr. Spear collaborated with Timothy McClintock, PhD, Louis Boyarsky Professor of Physiology, along with faculty in several College of Medicine departments including physiology and pharmacology and nutritional sciences. Together, they established the BERT workshop, a four-week course held entirely online through Zoom that taught rising second-year graduate students about useful technologies for analyzing large data sets. The workshop was geared toward the 21 students in the IBS program; however, 80 people signed up including College of Medicine faculty, post-docs, staff, and students, as well as students from the College of Pharmacy.
“The BERT workshop was a tremendous example of how passionate our faculty are about keeping our students on track,” Beth Garvy, PhD, associate dean for biomedical education, said. “The process took quick thinking and accelerated planning, and the result was successful in allowing our IBS students to remain engaged during the pandemic.”
BERT is an acronym standing for Bioinformatics, Excel, and R-programming tools, three topics emphasized in the workshop due to their prevalence in Dr. McClintock’s PGY 617 Physiological Genomics course for second-year graduate students embarking on their dissertation research. Though the focus of PGY 617 is on one particular type of large data set (gene expression data produced by RNA sequences or microarray techniques), the BERT workshop underlined the broad and valuable application of these tools in other data sets.
“We needed to make it clear to students that these tools would be valuable to them even if they never had to analyze transcriptome data produced by RNA sequences,” Dr. McClintock said. “In the end we continued to use transcriptome data as the primary examples in the workshop but tried to make it evident how the tools could be used more broadly.”
The bioinformatics portion of the BERT workshop showed students where to gain access to information about individual genes and proteins from the internet and taught them how to identify the most useful tools to analyze information. The Microsoft Excel portion of the workshop taught students to organize these large data sets through the use of spreadsheets. The R-programming portion trained students in programming skills for a language that is dedicated to statistical analysis of large data sets and visualization of these data.
Eric Blalock, PhD, associate professor in the department of pharmacology and nutritional sciences and master of analyzing transcriptome data, taught the Excel portion of the workshop. Dr. Sangderk Lee, PhD, assistant professor of pharmacology and nutritional sciences, assisted with the R-programming portion.
Dr. McClintock said that because PGY 617 is a computer lab course designed for hands-on training, the workshop was relatively simple to adapt to the cessation of face-to-face instruction. Also, PGY 617 is taught in spring semesters, so instructors had just moved their lectures and lab exercises into Zoom to provide the material the students need to complete the project assignments.
The experience of creating the workshop so quickly and efficiently under such dire circumstances helped Dr. Spear and Dr. McClintock realize the importance of taking action when recognizing a need.
“If there is one good thing that came from this COVID-19 experience, it forced us to act,” Dr. Spear said. “We had to act, and we had to act fast. This is not only true about courses, but also about other opportunities to train our students. I would say this experience really changed my attitude about how to get things accomplished.”
As of now, the material from the BERT workshop is being developed into a regular spring semester course for the IBS program, through which it can be useful to a wider range of students and the research laboratories they join.
“The BERT workshop will probably be a one-and-done event,” Dr. McClintock said. “But the players – bioinformatics, Excel tools, and R-programming – are moving on to the big leagues.”