Inimary Toby-Ogundeji, PhD
University of Dallas
The use of JupyterLab notebook provides a user-friendly method for learning data analysis. It is easy to work with and also provides a variety of datasets for direct use and case study data discussions. One example follow-up task that can be used to extend this data analysis activity is performing logistic regression. An example approach using Firth’s logistic regression method is provided here (https://bit.ly/31gb7vG). JupyterLab provides a temporary workspace to accomplish basic tasks in R. One consideration is that it doesn’t maintain the user’s data and/or work once they close the browser. Analysis performed in JupyterLab cannot be saved to the virtual platform, however files from the work session can be exported out and saved externally. For users wanting to have the capabilities of saving work sessions and transferring between JupyterLab sessions in a streamlined manner, they can establish a freely available account.
The activity described in this article highlight a user-friendly method to learn some basic data analysis skills. It is ideal for students with little to no experience in Biostatistics, Bioinformatics or Data Science. The article provides an opportunity for students to reflect and practice analysis of data collected from biological experiments within an online learning environment. The activity is suitable for an instructor led session (using an app with screen sharing capabilities). This article provides basic knowledge about how to use R for simple data analysis using the JupyterLab virtual notebook platform.
The goal of this activity is to familiarize the user with the basic steps for importing a data file, retrieval of file contents and generating a histogram using R within a JupyterLab environment. The workflow steps to accomplish these tasks are outlined below:
- Access JupyterLab
- Access “R”
- Access datasets
- Perform summary statistics
- Data visualization
Workflow Step-by-Step instructions and screenshots from JupyterLab
1. Access JupyterLab
a. Login to JupyterLab here: https://mybinder.org/v2/gh/jupyterlab/jupyterlab-demo/try.jupyter.org?urlpath=lab
2. Access “R”
a) Select the (+) symbol at the top left of the JupyterLab screen;
b) Select R
3. Access the dataset
a) Select the directory titled: “UPMC_cohort”;
b) Identify the filename “meta.csv”.
c) Type data<-read.csv(“meta.csv”,header=TRUE, stringsAsFactors-FALSE)
d) Click run
e) Type data
f) Click run
4. Perform summary statistics (on variable Cigarette_Pack_Years)
a) Type str(data)
b) Click run
c) Type data$Cigarette_Pack_Years
d) Click run
e) Type summary (data$Cigarette_Pack_Years)
f) Click run
5. Draw a histogram using the “hist” function
a) Type hist(data$Cigarette_Pack_Years, 100, main=”Use of Cigarette (in years)”, xlab=Cigarette Pack Years”, ylab”Frequency”)
b) Click run
R programming- https://www.r-project.org/
Dr. Toby holds a PhD in Biomedical Sciences (specialization in Organ Systems Biology) from Ohio State University, College of Medicine. Her postdoctoral training was in Functional Genomics at the FAA-Civil Aerospace Medical Institute in Oklahoma City. She is currently an Assistant Professor of Biology at University of Dallas. She teaches several courses including: Human Biology, Bioinformatics and Biostatistics. She enjoys mentoring undergraduate students and is an active member of The APS. Dr. Toby’s research program at UD is focused on cell signaling consequences that occur at the cellular/molecular interface of lung diseases. She is also leveraging the use of computational methods to assess immune sequencing and other types of high throughput sequencing data as a means to better understand lung diseases.
Andrew M. Roberts, M.S., Ph.D., FAPS
Department of Physiology
University of Louisville School of Medicine
Our graduate physiology courses at the University of Louisville School of Medicine evolved from a lecture-based format supplemented by recitation sessions and modules for each topic. Students work in groups to identify learning issues and discuss concepts needed to understand and solve assigned questions. They present their findings to the class and respond to questions from faculty and students. We found this to be an important forum whereby students gain experience applying their physiological knowledge.
An additional step that fostered student understanding was problem-based learning modules where student groups discussed and answered exam type questions. For the “pre-test” component, each group discussed and chose their answers together. This was followed by a “post-test” with different but, similar questions answered by each student individually. Our metrics clearly indicated students’ ability to apply their knowledge increased significantly.
Another component which bolstered student performance and encouraged use of multiple resources for information was online quiz questions for each learning module. Questions were made available on “Blackboard” and answered according to a schedule. Students received notification whether they answered correctly and could change their answer choices within an allotted time. Team-based learning with activities that encouraged students to incorporate multiple information sources improved students’ grasp of physiological concepts and mechanisms.
In summary, we developed ways to effectively engage our students who have diverse educational backgrounds and learning preferences. It is important to note that the classroom environment, with face to face instruction, provides the opportunity to teach and motivate students through interactions with faculty members and fellow students. However, other types of activities work well to augment and encourage student learning.
In the last year, our faculty has been discussing the possibility and usefulness of supplementing our program with online course options that could enhance students’ academic backgrounds whether they were on or off campus. Online learning has become prevalent as another teaching tool for a diverse student group and accommodates a variety of learning preferences. It offers flexibility whether used to supplement a “classroom” physiology course, or course taught exclusively online. Over the last year, our experience with online learning platforms indicated instructors could teach to an entire class simultaneously.
Students can be divided into discussion groups for problem-based learning and instructors can virtually interact by “joining” the groups. In addition, the platforms allow everyone to be seen and to be heard. Furthermore, it is easy to link slide as well as video presentations and record class sessions. Traditionally, we posted lecture notes and supplemental material on “Blackboard” for students to read before class and provided access to recorded lectures. There also is a forum for students to interact with each other and faculty members.
Educational methods are ever changing and can go forward and back again. With this in mind, online learning is not necessarily a replacement for face-to-face learning but, can be an additional learning tool. Even faculty less familiar with online learning have found the latest learning platforms to be relatively easy to use and actually to enhance their teaching styles. A key ingredient to the success of our program, is having designated faculty members and staff available as teaching resources! With the necessity for implementing social distancing during the COVID- 19 pandemic, online learning and video conferencing allowed us to continue and sustain our courses and academic program during this difficult time hopefully without jeopardizing student lifelong learning.
Andrew M. Roberts, MS, PhD, FAPS is an Associate Professor in the Department of Physiology at the University of Louisville School of Medicine in Louisville, Kentucky. He received his PhD in Physiology at New York Medical College and completed a postdoctoral training program in heart and vascular diseases, as well as, a Parker B. Francis Fellowship in Pulmonary Research at the University of California, San Francisco at the Cardiovascular Research Institute. His research focuses on cardiopulmonary regulatory mechanisms with an emphasis on neural control, microcirculation, and effects of local endogenous factors. Current studies include microvascular responses altered by inflammatory diseases and conditions, which can lead to acute respiratory distress syndrome. Additional studies include obstructive sleep apnea. He teaches physiology to graduate, medical, and dental students and has served as a course director as well as having taught allied health students.
Emilio Badoer, PhD
Professor of Neuropharmacology
School of Health & Biomedical Science with the College of Science, Engineering & Health
Royal Melbourne Institute of Technology (RMIT) University, Bundoora (Melbourne, Victoria, Australia)
Patricia A. Halpin, PhD
Associate Professor of Biological Science and Biotechnology & Visiting Associate Professor at RMIT University
Department of Life Sciences, University of New Hampshire at Manchester (Manchester, NH)
I was thrilled to spend my sabbatical performing education research at RMIT University in Australia during the spring semester of 2020. I met my collaborator Emilio Badoer at the APS ITL in 2016 and at that time we vowed to collaborate someday. I had a smooth flight to Melbourne AU and as we left the airport, I got my first view of the city covered in a smoky haze from the bushfires to the north1. The radio broadcast playing on the car stereo was alerting everyone to the tropical cyclones headed for the east coast and these would soon cause massive flooding in New South Wales. “Welcome to Australia” Emilio said, little did we know at the time that the worst was yet to come. The COVID-19 outbreak in China had caused Australia to close its borders on February 12,3 to foreign nationals who had left or transited through mainland China. I arrived February 9 and the focus of my attention was the excitement and anticipation of starting our two research projects. At my small college, my courses usually enroll 10-24 students, at RMIT our first study was working with a large nursing class (n =368) with the primary goal of using Twitter to engage them outside of class with the course content.
The nursing cohort started two weeks prior to the start of the term, and in the third week, the students went on clinical placements for five weeks. This course is team-taught and Emilio taught during the first two-week period so that content was the focus of our research for this study. We designed the study to collect data using paper surveys to be distributed at face-to-face class meetings at the beginning and end of the term to ensure a high rate of survey completion. The second study performed with his Pharmacology of Therapeutics class (n=140) started on March 2 with one face-to-face meeting followed by four weeks of flipped teaching (FT). During the FT period, we would engage them on Twitter with course content and they would meet during weekly face-to-face Lectorial sessions for review during the usual scheduled class time. Students completed the paper pre-survey in the first class meeting and the scheduled paper post-surveys were to be distributed during the final Lectorial sessions on March 19 and 20. Then on Monday March 16th everything changed; Victoria declared a state of emergency to combat the COVID-19 pandemic4 and Qantas announced that they would cancel 90% of their international flights5, with the remaining flights cancelled on March 31.
I was contacted by friends and family back home urging me to come home right away. RMIT announced the decision that learning would go online starting March 23. In the United States, colleges had previously announced that students heading home for spring break should stay home as their classes would be delivered online due to the COVID-19 concerns 6. The faculty at the US schools had spring break to prepare the transition of their course content for the new delivery mode. At RMIT, they had recently started their semester with no spring break normally scheduled and the only break on the horizon was the distant Easter holiday (April 10-13) long weekend. Our hopes for data collection were quickly dashed as during the last Lectorial sessions only a few students attended, and we would not be able to survey the nursing students in person when they returned from placements.
My focus shifted to leaving the country as soon as possible. The only way to change my airline ticket home was through a travel agent and my personal travel agent spent a total of 11.5 h on hold with Qantas over a two-day period to secure my ticket home. I left Australia with hordes of anxious Americans. The airports were overwhelmed as we formed long lines trying to check in and then go through security. Everyone had a story to tell of how they had to cut their trip short and then changed their tickets. In Los Angeles I was joined by more Americans who were coming from New Zealand. Many of the American travelers were undergraduates very disappointed that their universities had called them home and they were leaving their semester abroad adventures. We would all soon arrive home safely to a country living in a new reality.
Meanwhile, in Australia, the situation at universities evolved rapidly. In line with the Australian Government mandate, students were told that all new arrivals into the country must self-isolate for 14 days effective March 16. Public gatherings of over 500 people were no longer allowed. Although universities were specifically exempt from this requirement, RMIT University proactively cancelled or postponed any events that were not related to the core business of learning, teaching and research. It also foreshadowed a progressive transition to lectures being delivered online where possible. The University also indicated that students would not be disadvantaged if they chose not to attend face-to-face classes during the week of March 16. In response to the rapid changes occurring internationally, on March 20, the Australian Government restricted all non-Australian citizens and non-Australian residents from entering the country. While Australian Universities could remain open and operating it was clear that this would not last for long 7. In response, RMIT University mandated that from Monday March 23 lectures were to be made available online but tutorials and seminars and non-specialist workshops could continue face-to-face until March 30.
On Sunday March 22 the State Government of Victoria (where the main RMIT University campus is based) mandated the shutdown of all non-essential activity from Tuesday March 24 to combat the spread of COVID-19 7. Immediately, RMIT University suspended all face-to-face learning and teaching activity on all its Australian campuses. Overnight, faculty became online teaching facilitators. Emilio produced and is continuing to produce new videos (15-30 minutes duration) covering the content normally delivered during the face-to-face large lecture session. Each week 3-5 videos are produced and uploaded onto Canvas (RMIT’s online learning management system) for the students.
Unlike many of the US schools that are using Zoom, RMIT is using Collaborate Ultra within Canvas as its way of connecting with students on a weekly basis. Collaborate Ultra has the ability to create breakout groups and faculty can assign students to a specific breakout group or allow students to self-allocate to a specific breakout group. Emilio has allowed students to move between breakout groups to increase engagement. The only stipulation was to limit the group size usually to no more than six. Each student was originally registered to attend one small group Lectorial session that meets once per week for one hour and these groups have between 45-50 students each. The Lectorials were replaced by Collaborate Ultra sessions that were organized for the same times and dates as the normally scheduled small Lectorial sessions. The students and facilitators would all meet in the so-called “main room” where Emilio would outline the plans for the session. The main room session was conducted with Emilio’s video turned on so the students were ‘invited “into his home” and could feel connected with him. Dress code was also important. Emilio was conscious of wearing smart casual apparel as he would have worn had he been facing the students in a face-to-face session. In this way he attempted to simulate the normal pre-COVID-19 environment.
Following the introductory remarks outlining the tasks for the session, students were ‘sent’ to their breakout rooms to discuss and work on the first problem / task discussed in the main room. The analogy used by Emilio was that the breakout rooms were akin to the tables that were used in their collaborative teaching space in which he normally conducted the Lectorial sessions. Each table in that space accommodated approximately six students (hence the stipulation of no more than six in each breakout group). Emilio and another moderator ‘popped’ into each breakout room to guide and facilitate the students in their discussions. To date, the level of engagement and discussion amongst the students themselves generally appears to be much greater than that observed at face-to-face sessions which was a fantastic surprise. After a set time had elapsed, students re-assembled in the main room where the task was discussed with the whole class. This ensured that all students understood the requirements of the task and they had addressed all points that were needed to complete the task to the satisfactory standard. Next followed another task that differed from the first providing variety and maintaining the interest of the students.
Examples of tasks performed.
1 – Practice exam questions
A short answer question requiring a detailed response that would normally take at least 10 minutes in an exam environment to answer properly. Such questions were based on that week’s lecture (now video) course content and was contextualized in a scenario in which physiological/pathophysiological conditions were described and the pharmacological treatments needed to be discussed in terms of mechanisms of action, adverse effects, potential drug interactions or pharmacogenomic influences etc.
2 – Multiple choice questions – Quizzes
Emilio ran these using the Kahoot platform. By sharing his screen, Emilio could conduct such quizzes live providing instant feedback on student progress. This allowed Emilio to provide formative feedback, correct any misconceptions and discuss topics. Additionally, students were able to gauge their own learning progress. These tasks were performed in the main room with all participants.
3 – Completing sentences or matching answers
These could be done effectively in the breakout rooms, where a ‘lead’ student could utilize the whiteboard function in Collaborate Ultra which allowed all students in the group the opportunity to write on the whiteboard allowing discussion regarding the answers written.
4 – Filling in the gaps
Here Emilio would share his screen in which a diagram / figure / a schematic of a pathway etc. with labels/ information missing was provided and students were asked to screenshot the shared information. Then in breakout rooms, one student shared the captured screen shot with the group and the missing information was completed by the members of the group.
The Collaborate Ultra sessions were also utilized to provide students with a platform in which group work could be performed. With a lockdown in force and gatherings of groups forbidden, this utility was very important for enabling connection between students working on group projects. It also provided a sense of belonging within the student cohort.
In conclusion, with minimal preparation, a huge Australian University converted face-to-face teaching and learning to an online digital teaching and learning environment where working remotely was the new norm. It is almost inconceivable just a few short weeks ago that such a transformation could have happened in the timeframe that it did. It is a truly remarkable achievement.
1 Alexander, H and Moir N. (December 20, 2019). ‘The monster’: a short history of Australia’s biggest forest fire. Sydney Morning Herald Retrieved on April 10, 2020 from https://www.smh.com.au/national/nsw/the-monster-a-short-history-of-australia-s-biggest-forest-fire-20191218-p53l4y.html
2 Statement on the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV) (Jan. 30, 2020). Retrieved on April 10, 2020 from https://www.who.int/news-room/detail/30-01-2020-statement-on-the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov)
3 Travel Restrictions on China Due to COVID-19 (April 6, 2020). Retrieved on April 10, 2020 from https://www.thinkglobalhealth.org/article/travel-restrictions-china-due-covid-19
4 Premier of Victoria, State of Emergency Declared in Victoria Over COVID-19. (March 16, 2020) Retrieved on April 10, 2020 from https://www.premier.vic.gov.au/state-of-emergency-declared-in-victoria-over-covid-19/
5 Qantas and Jetstar slash 90 per cent of international flights due to corona virus (March 16, 2020). Retrieved on April 10, 2020 from https://www.abc.net.au/news/2020-03-17/qantas-coronavirus-cuts-capacity-by-90-per-cent/12062328
6 Hartocollis A. (March 11, 2020). ‘An Eviction Notice’: Chaos After Colleges Tell Students to Stay Away. The New York Times. Retrieved on April 10, 2020 from https://www.nytimes.com/2020/03/11/us/colleges-cancel-classes-coronavirus.html
7 Worthington B (March 22, 2020). Coronavirus crackdown to force mass closures of pubs, clubs, churches and indoor sporting venues. Retrieved on April 10, 2020 from https://www.abc.net.au/news/2020-03-22/major-coronavirus-crackdown-to-close-churches-pubs-clubs/12079610
Professor Badoer has held numerous teaching and learning leadership roles including many years as the Program Coordinator for the undergraduate Pharmaceutical Sciences Program at RMIT University in Bundoora AU and he coordinates several courses. He is an innovative instructor that enjoys the interactions with students and teaching scholarship. He has also taught pharmacology and physiology at Melbourne and Monash Universities. In addition, he supervises several postgraduate students, Honours students and Postdoctoral Fellows.
Patricia A. Halpin is an Associate Professor in the Life Sciences Department at the University of New Hampshire at Manchester (UNHM). Patricia received her MS and Ph.D. in Physiology at the University of Connecticut. She completed a postdoctoral fellowship at Dartmouth Medical School. After completion of her postdoc she started a family and taught as an adjunct at several NH colleges. She then became a Lecturer at UNHM before becoming an Assistant Professor. She teaches Principles of Biology, Endocrinology, Cell Biology, Animal Physiology, Global Science Explorations and Senior Seminar to undergraduates. She has been a member of APS since 1994 and is currently on the APS Education committee and is active in the Teaching Section. She has participated in Physiology Understanding (PhUn) week at the elementary school level in the US and Australia. She has presented her work on PhUn week, Using Twitter for Science Discussions, and Embedding Professional Skills into Science curriculum at the Experimental Biology meeting and the APS Institute on Teaching and Learning.
Ida T. Fonkoue, Ph.D.
Post-Doctoral Fellow, Renal Division
Emory University School of Medicine
Ramon A. Fonkoue, Ph.D.
Associate Professor, French and Cultural Studies
Michigan Technological University
The COVID-19 pandemic has led to a total and sudden reshaping of the academic landscape across the country, with hundreds of institutions moving administration entirely online and shifting to online instruction for the remainder of the spring semester or for both spring and summer. This sudden transition with practically no time to prepare has major implications for students and faculty alike, and poses serious challenges to a smooth transition as well as effective online teaching on such a large scale. Out of these challenges, two issues in particular are examined here:
- the disparity in resources and preparedness for effective online teaching
- the implications of the migration to virtual classrooms for diversity and inclusion
Disparity in resources and preparedness for effective online teaching
Teaching an online course requires just as much, if not more, time and energy as traditional classroom courses. It also requires specific IT skills to be effective. Some teachers have managed to achieve great success engaging students online. However, many challenges remain for the average teacher. While online teaching has now been embraced by all higher education institutions and the number of classes offered online has seen a steady growth over the years, it should be noted that until now, instructors and students had the choice between brick and mortar classes and virtual ones. Each could then choose based on their personal preferences and/or circumstances. What makes the recent changes so impactful and consequential is that no choice is left to instructors or students, as the move to online classes is a mandate from the higher administration. Whether one is willing, prepared or ready is irrelevant. It is from this perspective that the question of the preparedness to migrate online is worth examining.
With academic units ordered to move classes online, instructors who had remained indifferent to the growing trend of online teaching have had a difficult reckoning. They have had to hastily move to online delivery, often with a steep learning curve. This challenge has been compounded in some cases by the technology gap for instructors who haven’t kept their IT skills up to date as well as the school’s preparedness to support online teaching. But even instructors who had some familiarity with learning management systems (LMS) and online delivery have faced their share of challenges. We will only mention two sources of these difficulties:
- First, students’ expectations in a context of exclusive online teaching are different from when most online classes took place in the summer, and were attractive to students because of convenience and flexibility. With online classes becoming the norm, students in some universities are taking steps to demand that school administrators pay more attention to quality of instruction and maintain high standards to preserve teaching effectiveness.
- Second, instructors can no longer use LMS resources just for the flexibility and benefits they afforded, such as in blended classes or flipped classes. Moving everything online thus requires extra work even for LMS enthusiasts.
For students, there have been some interesting lessons. Until now, it was assumed that Generation Z students (raised in the boom of the internet and social media) we have in our classes have tech skills in their DNA and would be well equipped and ready to migrate online. Surprisingly, this hasn’t been the case across the board, and these first weeks have revealed real discrepancies in student IT equipment with varying consequences for online classes. Equipment failure and problems with access to high speed internet emerge as the most serious difficulties on the students’ side. Furthermore, online learning requires independence and often more self-discipline and self-motivation. Most online courses are not taught in real time, and there are often no set times for classes. While this flexibility makes online classes attractive, it can also be a drawback for students who procrastinate and are unable to follow the course pace. If left to themselves, only the most responsible students will preserve their chances of performing well. On this last point, one unexpected issue has been students who have virtually disappeared from their classes since the migration of courses online amid the COVID-19 pandemic. The current transition has thus presented major challenges for teachers and students alike.
Implications of the migration to virtual classrooms for diversity and inclusion
The second issue we think deserves attention is the way in which educational institutions’ commitment to diversity and inclusion would play out in virtual classes. While they are now among the professed core values of all colleges and universities across the country, implementing diversity and inclusion in an online environment presents a different set of challenges for both instructors and students. In traditional classrooms, the commitment to diversity and inclusion typically translates into the following:
- A diversity and inclusion statement from the school must be included in the course syllabus.
- Instructors must remind students a few rules at the beginning of the course, including: recognition that the classroom is an environment where diversity is acknowledged and valued; tolerance of and respect for diversity of views in the classroom.
- Sensitivity to and respect for diversity (gender, age, sexual orientation, etc.).
- Students are asked to be courteous and respectful of different opinions.
In moving into a virtual environment, instructors have to think about the challenges of virtual classrooms and their potential impact on diversity and inclusion. For instance, the faceless nature of course participation and asynchronous delivery may make it easier for participants to disregard or neglect diversity and inclusion rules. Teachers need to reflect on ways to ensure that the virtual space of online classes remains an environment that fosters diversity and inclusion. One drawback of online classes is the potential impact of the relative anonymity on social engagement. In a traditional classroom, participants are constrained by the physical presence of their peers in the confined space of the classroom. The closed physical space of the classroom, combined with the instructor’s authority and peer pressure contribute to fostering discipline. Reflecting on the way online teaching impacts the instructor, one faculty noted: “I didn’t realize how much I rely on walking around the room and making eye contact with students to keep them engaged.” As an online teacher, one lacks the ability to connect physically with students, to read emotional cues and body language that might inform about the individuality of a student. Moreover, a good grasp of the diversity in the classroom and of students’ learning abilities is needed to plan instruction, and give each of them the opportunity to learn and succeed.
Drawing from the above considerations, here are some key questions that instructors should consider as they migrate online: What skills do instructors need to properly address diversity and inclusion online? How do instructors include diversity and inclusion requirements in online course design? How to create an inclusive online classroom? How do instructors attend to diverse students’ needs during instruction? How do they monitor behaviors and enforce diversity and inclusion rules during instruction?
While the migration might have been abrupt, instructors need not seek perfection in moving their courses online. As in traditional classes, what matters the most, from the student’s point of view, is constant communication, clear directions and support from their teachers. Students understand the challenges we all face. They also understand the rules in virtual classes, provided we emphasize them.
Hill, Phil (2020), Massive Increase in LMS and Synchronous Video Usage Due to COVID-19. PhilonEdTech. https://philonedtech.com/massive-increase-in-lms-and-synchronous-video-usage-due-to-covid-19/
Greeno, Nathan (2020), Prepare to Move Online (in a Hurry). Inside Higher Ed. https://www.insidehighered.com/views/2020/03/10/prepare-move-online-continuity-planning-coronavirus-and-beyond-opinion
McMurtrie, Beth (2020), The Coronavirus Has Pushed Courses Online. Professors Are Trying Hard to Keep Up. The Chronicle of Higher Education. https://www.chronicle.com/article/The-Coronavirus-Has-Pushed/248299
Dr Ida Fonkoué is a post-doctoral fellow at Emory University School of Medicine in the Laboratory of Dr Jeanie Park. She trained under Dr Jason Carter at Michigan Technological University, where she graduated with a PhD in Biological Sciences in December 2016. She teaches renal physiology classes and lead small groups in the School of Medicine. Her long-term research goal is to understand how the sympathetic nervous system, the vasculature and inflammation interplay to contribute to the high cardiovascular disease risk of patients living with chronic stress, such as those with post-traumatic stress disorder.
Dr. Ramon A Fonkoué is an Associate Professor of French and Cultural Studies and the Director of Graduate Studies in the Department of Humanities at Michigan Technological University. He is also a Visiting Scholar in the department of French and Italian at Emory University. He has been teaching online for 9 years and has experience with blended, flipped and full online classes.
Last summer, some colleagues and I published a paper on how high school students can communicate their understanding of science through songwriting. This gradually led to a press release from my home institution, and then (months later) a feature article in a local newspaper, and then appearances on Seattle TV stations KING-5 and KOMO-4.
It’s been an interesting little journey. I haven’t exactly “gone viral” — I haven’t been adding hundreds of new Twitter followers, or anything like that — but even this mild uptick in interest has prompted me to ponder my relationship with the news media. In short, I do enjoy the attention, but I also feel some responsibility to influence the tone and emphases of these stories. In this post, I share a few bits of advice based on my recent experiences, and I invite others to contribute their own tips in the comments section.
(1) Find out how your school/department/committee views media appearances. In April, I was invited to appear on KING’s mid-morning talk show, which sounded cool, except that the show would be taped during my normal Thursday physiology lecture! My department chair and my dean encouraged me to do the show, noting that this sort of media exposure is generally good for the school, and so, with their blessing, I got a sub and headed for the studio.
(2) Respect students’ privacy during classroom visits. After some students were included in a classroom-visit video despite promises to the contrary, I realized that I needed to protect their privacy more strongly. I subsequently established an option by which any camera-shy students could live-stream the lecture until the TV crew left.
(3) Anticipate and explicitly address potential misconceptions about what you’re doing. I’ve worried that these “singing professor” pieces might portray the students simply as amused audience members rather than as active participants, so, during the classroom visits, I’ve used songs that are conducive to the students singing along and/or analyzing the meaning of the lyrics. (Well, mostly. “Cross-Bridges Over Troubled Water” wasn’t that great for either, but I had already sung “Myofibrils” for KING, and KOMO deserved an exclusive too, right?)
(4) Take advantage of your institution’s public relations expertise. Everett Community College’s director of public relations offered to help me rehearse for the talk show — and boy am I glad that she did! Being familiar with the conventions and expectations of TV conversations, Katherine helped me talk much more pithily than I normally do. In taking multiple cracks at her practice question about “how did you get started [using music in teaching]?” I eventually pared a meandering 90-second draft answer down to 30 seconds. She also asked me a practice question to which my normal response would be, “Can you clarify what you mean by X?” — and convinced me that in a 4-minute TV conversation, you don’t ask for clarifications, you just make reasonable assumptions and plow ahead with your answers.
(5) Ask your interviewers what they will want to talk about. Like a novice debater, I struggle with extemporaneous speaking; the more I can prepare for specific questions, the better. Fortunately, my interviewers have been happy to give me a heads-up about possible questions, thus increasing their chances of getting compelling and focused answers.
Readers, what other advice would you add to the above?
Gregory J. Crowther, PhD has a BA in Biology from Williams College, a MA in Science Education from Western Governors University, and a PhD in Physiology & Biophysics from the University of Washington. He teaches anatomy and physiology in the Department of Life Sciences at Everett Community College. His peer-reviewed journal articles on enhancing learning with content-rich music have collectively been cited over 100 times.
by Jessica M. Ibarra
I always had this curiosity about life. Since the very beginning, always wanting to understand how animals’ breathe, how they live, how they move. All that was living was very interesting. – Dr. Ibarra
“I always had this curiosity about life and I wanted to become a doctor, but my parent told me it was not a good idea,” Lise Bankir explained in her interview for the Living History Project of the American Physiological Society (APS). The video interview (video length: 37.14 min.) is part of a rich collection over 100 senior members of the APS who have made outstanding contributions to the science of physiology and the profession.
The archive gives us great insight into how these scientists chose their fields of study. As Dr. Bankir, an accomplished renal physiologist, explain how she ended up “studying the consequences of vasopressin on the kidney.” She describes her work in a 1984 paper realizing “high protein was deleterious for the kidney, because it induces hyperfiltration,” which of course now we accept that high protein accelerates the progression of kidney disease. Later she describes her Aha! moment, linking a high protein diet to urea concentration, while on holiday.
“It came to my mind that this adverse effect of high protein diet was due to the fact that the kidney not only to excrete urea (which is the end product of proteins), but also to concentrate urea in the urine. Because the plasma level of urea is already really low and the daily load of urea that humans excrete need that urea be concentrated about 100-fold (in the urine with respect to plasma).”
Other interviews highlight how far ahead of their time other scientists were. As is the case when it comes to being way ahead of teaching innovations and active learning in physiology with Dr. Beverly Bishop. In her video interview, you can take inspiration from her 50 years of teaching neurophysiology to physical therapy and dental students at SUNY in New York (video length: 1 hr. 06.09 min.). Learn about how she met her husband, how she started her career, and her time in Scotland. Dr. Bishop believed students could learn better with experimental laboratory activities and years ahead of YouTube, she developed a series of “Illustrated Lectures in Neurophysiology” available through APS to help faculty worldwide.
She was even way ahead of others in the field of neurophysiology. Dr. Bishop explains, “everyone knows that they (expiratory muscles) are not very active when you are sitting around breathing quietly, and yet the minute you have to increase ventilation (for whatever reason), the abdominal muscles have to play a part to have active expiration. So, the question I had to answer was, “How are those muscles smart enough to know enough to turn on?” Her work led to ground breaking work in neural control of the respiratory muscles, neural plasticity, jaw movements, and masticatory muscle activity.
Another interview shed light on a successful career of discovery and their implications to understanding disease, as is the case with the video interview of Dr. Judith S. Bond. She describes the discovery of meprins proteases as her most significant contribution to science (video length: 37.38 min.), “and as you know, both in terms of kidney disease and intestinal disease, we have found very specific functions of the protease. And uh, one of the functions, in terms of the intestinal disease relates to uh inflammatory bowel disease. One of the subunits, meprin, alpha subunit, is a candidate gene for IBD and particularly ulcerative colitis. And so that opens up a window to – that might have significance to the treatment of ulcerative colitis.”
Or perhaps you may want to know about the life and research of Dr. Bodil Schmidt-Nielsen, the first woman president of the APS (video length: 1 hr. 18.07 min.) and daughter of August and Marie Krogh. In her interview, she describes her transition from dentistry to field work to study water balance on desert animals and how she took her family in a van to the Arizona desert and while pregnant developed a desert laboratory and measured water loss in kangaroo rats. Dr. Schmidt-Nielsen was attracted to the early discoveries she made in desert animals, namely that these animals had specific adaptations to reduce their expenditure of water to an absolute minimum to survive.
The Living History Project managed to secure video interviews with so many outstanding contributors to physiology including John B. West, Francois Abboud, Charles Tipton, Barbara Horwitz, Lois Jane Heller, and L. Gabriel Navar to name a few. For years to come, the archive provides the opportunity to learn from their collective wisdom, discoveries, family influences, career paths, and entries into science.
As the 15th anniversary of the project approaches, we celebrate the life, contributions, dedication, ingenuity, and passion for science shared by this distinguished group of physiologists. It is my hope you find inspiration, renewed interest, and feed your curiosity for science by taking the time to watch a few of these video interviews.
Dr. Jessica M. Ibarra is an Assistant Professor of Physiology at Dell Medical School in the Department of Medical Education of The University of Texas at Austin. She teaches physiology to first year medical students. She earned her B.S. in Biology from the University of Texas at San Antonio. Subsequently, she pursued her Ph.D. studies at the University of Texas Health Science Center in San Antonio where she also completed a postdoctoral fellowship. Her research studies explored cardiac extracellular matrix remodeling and inflammatory factors involved in chronic diseases such as arthritis and diabetes. When she is not teaching, she inspires students to be curious about science during Physiology Understanding Week in the hopes of inspiring the next generation of scientists and physicians. Dr. Ibarra is a native of San Antonio and is married to Armando Ibarra. Together they are the proud parents of three adult children – Ryan, Brianna, and Christian Ibarra.
Teaching a large (nearly 400 students), introductory survey course in human anatomy and physiology is a lot like trying to hit a constantly moving target. Once you work out a solution or better path for one issue, a new one takes its place. You could also imagine a roulette wheel with the following slots: student-faculty ratios, student preparation, increasing enrollments, finite resources, limited dissection specimen availability (e.g., cats), textbook prices, online homework, assessment, adaptive courseware, core competencies, learning outcomes, engagement, supplemental instruction, prerequisites, DFW rates, teaching assistants, Dunning Kruger effect, open educational resources, GroupMe, student motivation, encouraging good study habits, core concepts, aging equipment … and the list goes on.
If the ball lands on your slot, are you a winner or loser?
Before getting ahead of myself, I need to provide an overview of A&P at the University of Mississippi. Fall semesters start with 390 students enrolled in A&P I within one lecture section, 13 lab sections at 30 students each, anywhere from 10-13 undergraduate teaching assistants, 2 supplemental instruction (SI) leaders, and at least six, one-hour SI sessions each week. The unusual class size and number of lab sections is the result of maxing out lecture auditorium as well as lab classroom capacities. I am typically the only instructor during the fall (A&P I) and spring (A&P II) terms, while a colleague teaches during the summer terms. The two courses are at the sophomore-level and can be used to fulfill general education requirements. There are no prerequisites for A&P I, but students must earn a C or better in A&P I to move on to A&P II. Approximately one-third of the students are allied health (e.g., pre-nursing) and nutrition majors, one-third are exercise science majors, and the remaining one-third of students could be majoring in anything from traditional sciences (e.g., Biology, Chemistry, etc.) to mathematics or art.
The university supports a Supplemental Instruction program through the Center for Excellence in Teaching and Learning (https://cetl.olemiss.edu/supplemental-instruction/). The SI program provides an extra boost for students in historically demanding courses such as freshman biology, chemistry, physics, accounting, etc. SI leaders have successfully passed the courses with a grade of B or better, have been recommended to the program by their professors, agree to attend all lectures for the courses in which they will be an SI leader, and offer three weekly, one-hour guided study sessions that are free to all students enrolled in the course. SI leaders undergo training through Center for Excellence in Teaching and Learning and meet weekly with the course professor. Students who regularly attend SI sessions perform one-letter grade higher than students who do not attend SI sessions.
It can be as easy for an instructor to be overwhelmed by the teaching side of A&P as it is for the student to be overwhelmed by the learning side! I know that a major key to student success in anatomy and physiology courses is consistent, mental retrieval practice across multiple formats (e.g., lectures, labs, diagrams, models, dissection specimens, etc.). The more a student practices retrieving and using straightforward information, albeit a lot of it, the more likely a student will develop consistent, correct use. Self-discipline is required to learn that there are multiple examples, rather than one, of “normal” anatomy and physiology. However, few students know what disciplined study means beyond reading the book and going over their notes a few times.
To provide a model for disciplined study that can be used and implemented by all students, I developed weekly study plans for A&P I and II. These study plans list a variety of required as well as optional activities and assignments, many of which are completed using our online courseware (Pearson’s Mastering A&P) and include space for students to write completion dates. If students complete each task, they would spend approximately 10 out-of-class hours in focused, manageable activities such as:
- Completion of active learning worksheets that correlate to learning outcomes and can be used as flashcards.
- Practice assignments that can be taken multiple times in preparation for lecture exams and lab practicals.
- Self-study using the virtual cadaver, photographic atlas of anatomical models, interactive animations of physiological processes, virtual lab experiments, and dissection videos.
- Regular graded assignments aligned with course learning outcomes.
Weekly study plans are also useful during office visits with students. I can easily assess student progress and identify changes for immediate and long-term improvement. An advantage of using online courseware to support course objectives is the ability to link various elements of the courses (e.g., lecture, lab, SI sessions, online homework, group study, and self-study) with a consistent platform.
All of this sounds like a great sequence of courses, doesn’t it? Yet, the target has kept moving and the roulette wheel has kept spinning. Imagine for the story within this blog that the roulette ball has landed on “using adaptive courseware to improve supplemental instruction.”
In 2016 the University of Mississippi was one of eight universities chosen by the Bill and Melinda Gates Foundation with support of the Association for Public and Land-Grant Universities to increase the use of adaptive courseware in historically demanding general education courses. Thus, began the university’s PLATO (Personalized Learning & Adaptive Teaching Opportunities) Program (https://plato.olemiss.edu/). The PLATO grant provides support for instructors to effectively incorporate adaptive courseware into their courses and personalize learning for all affected students. Administrators of the grant were particularly supportive of instructors who could use adaptive courseware to support the SI sessions. This challenge was my personal roulette ball.
I decided to use diagnostic results from Mastering A&P graded homework assignments to prepare for weekly meetings with SI leaders. Diagnostic data on percent of University of Mississippi students correctly answering each question as well as percent of UM students answering incorrect options are compared to the global performance of all Mastering A&P users. For each question incorrectly answered by more than 50% of the students, I write a short (4-6 sentences) explanation of where students are making errors in expressing or using their knowledge and how to prevent similar errors in the future. I then searched for active learning activities and teaching tips associated with the challenging questions from the LifeSciTRC (https://www.lifescitrc.org/) and Human Anatomy and Physiology Society (HAPS; https://www.hapsweb.org/) websites. I specifically search for active learning exercises that can be conducted in a small, group setting using widely available classroom resources (e.g., white board, sticky notes, the students, etc.).
By using online courseware diagnostics, selecting focused learning activities, and communicating regularly with SI leaders, I was able to create value and unique learning opportunities for each student. The SI session format has been extremely well-received by the students and they immediately see the purpose in the study session experience. The best part is that it takes me only 30-40 minutes each week to write up explanations for the diagnostics and find the best learning activities.
I would say that we are all winners with this spin of the wheel.
Recently I was faced with a teaching challenge: how to incorporate active learning in a huge Introductory Biology lecture of 400+ students. After searching for methods that would be feasible, cost effective, and reasonably simple to implement in the auditorium in which I was teaching, I came up with clickers. Our university has a site license for Reef Polling Software which means I wouldn’t add to the cost for my students—they could use any WiFi enabled device or borrow a handset at no cost. I incorporated at least 4 clicker questions into every class and gave students points for completing the questions. 10% of their grade came from clicker questions and students could get full credit for the day if they answered at least 75% of the questions. I did not give them points for correct answers because I wanted to see what they were struggling to understand.
I’m now a clicker convert for the following 3 reasons:
- Clickers Increase Student Engagement and Attendance
In a class of 400+, it is easy to feel like there is no downside to skipping class since the teacher won’t realize you are gone. By attaching points to completing in-class clicker questions, about 80% of the class attended each day. While I would like perfect attendance, anecdotally this is much better than what my colleagues report for similar classes that don’t use clickers. Students still surfed the internet and slept through class, but there was now more incentive to pay a bit of attention so you didn’t miss the clicker questions. In my opinion, getting to class can be half the battle so the incentive is worth it. In my small classes I like to ask a lot of questions and have students either shout out answers or vote by raising their hands. Often, students won’t all vote or seem to be too embarrassed to choose an answer. I tested out clickers in my small class and found an increased response rate to my questions and that I was more likely to see the full range of student understanding.
- Clickers Help Identify Student Misconceptions in Real Time
Probably the biggest benefit of clickers to my teaching is getting a better sense of what the students are understanding in real time. Many times I put in questions that I thought were ‘gimmes’ and was surprised to see half the class or more getting them wrong. When that happens, I can try giving them a hint or explaining the problem in a different way, having them talk with their group, and then asking them to re-vote. Since I don’t give points for correctness, students don’t feel as pressured and can focus on trying to understand the question. I’m often surprised that students struggle with certain questions. For instance, when asked whether the inner membrane of the mitochondria increases surface area, volume, or both, only half of the students got the correct answer the first time (picture). Since this is a fundamental concept in many areas of biology, seeing their responses made me take time to really explain the right answer and come up with better ways of explaining and visualizing the concept for future semesters.
- Clickers Increase Student Learning (I hope)
At the end of the day, what I really hope any active learning strategy I use is doing is helping students better understand the material. To try to facilitate this, I ask students to work in groups to solve the problems. I walk around the class and listen while they solve the problem. This can help me get an idea of their misconceptions, encourage participation, and provide a less scary way for students to ask questions and interact with me. While working in groups they are explaining their reasoning and learning from each other. Interspersing clicker questions also helps to reinforce the material and make sure students stay engaged.
I’m convinced that clickers are helping to improve my teaching and students seem to agree. Of the 320 students who filled out course evaluations one semester, 76 included positive comments about clicker questions. Here are two of my favorites:
“I like how we had the in-class clicker questions because it made me think harder about the material we were learning about in that moment.”
“I enjoyed doing the clicker questions. If the class disagreed with something she would stop and reteach the main point and hope we would understand. That was really helpful on her part.”
I would be remiss if I didn’t end by thanking the many researchers who have studied how to incorporate clickers into your class to maximize learning. I decided to try them after hearing Michelle Smith talk at the first APS Institute on Teaching and Learning and highly recommend seeing her speak if you have the chance. If you only want to read one paper, I suggest the following:
Smith, Michelle K., et al. “Why peer discussion improves student performance on in-class concept questions.” Science 323.5910 (2009): 122-124.
I hope you will comment with how you use clickers or other strategies to engage large lecture classes. For more resources I’ve found helpful designing my classes click here.
|Katie Wilkinson, PhD is a newly minted Associate Professor of Biological Sciences at San Jose State University. She completed her undergraduate work in Neuroscience at the University of Pittsburgh and her PhD in Biomedical Sciences at the University of California, San Diego. She was an NIH IRACDA Postdoctoral Fellow in Research and Scientific Teaching at Emory University. At SJSU her lab studies the function of stretch sensitive muscle proprioceptors. She teaches Introductory Biology, Vertebrate Neurophysiology, Integrative Physiology, Pain Physiology, and Cardiorespiratory Physiology to undergraduate and masters students.|
When I was approached to write a blog for PECOP I thought I could bring a slightly different perspective on classroom technology as I am not a full-time classroom educator. My primary role for the past dozen years with ADInstruments has been to work with educators who use our products to get the most from their investment in our technology. This has led to thousands of conversations about use and misuse of technology in the classroom and teaching laboratories. I would like to share some of my insights here.
Early in my academic career I was tasked with a major overhaul of the introductory Biology curriculum at Louisiana Tech, and incorporating technology was part of this mandate. I have always been a bit of a tech geek, but rarely an early adopter. I spent quite a bit of time and effort taking a good hard look at technology before implementing it in my classrooms. I was fortunate enough to participate in T.H.E. QUEST (Technology in Higher Education: Quality Education for Students and Teachers). Technology was just beginning to creep into the classroom in the late nineties. Most courses were traditional, chalk and talk; PowerPoint was still a new thing, and this three-week course taught us how to incorporate this emerging technology appropriately. PowerPoint worked better for many of us than chalk and talk, but also became a crutch, and many educators failed to use the best parts of this technology and applied it as a panacea. Now PowerPoint has fallen out of favor and has been deemed to be “Killing Education”(1). When used improperly, rather than curing a problem, it has backfired and reduced complex concepts to lists and bullet points.
I was fortunate enough to have been on the leading edge for a number of technologies in both my graduate and academic careers. Anybody remember when thermocyclers were rare and expensive? Now Open PCR can deliver research quality DNA amplification for around $500. Other technologies became quickly obsolete; anybody remember Zip drives? Picking the tech that will persist and extend is not an easy task. Will the Microscope go the way of the zip drive? For medical education this is already happening (2). While ADInstruments continues to lead the way with our PowerLab hardware and software packages for education (3); there are plenty of other options available. Racks of very specialized equipment for recording biological signals can now be replaced with very affordable Arduino based electronics (4,5). As these technologies and their supporting software gets easier to use, almost anyone can collect quality physiological data.
One of the more interesting technologies that is evolving rapidly is the area of content delivery or “teaching and learning” platforms. The most common of these for academia are the Learning Management Systems. These are generally purchased by institutions or institutional systems and “forced” upon the faculty. I have had to use many different platforms at different institutions. Blackboard, Desire 2 Learn, Moodle, etc. are all powerful tools for managing student’s digital records, and placing content in their “virtual” hands. Automatic grading of quiz questions, as well as built in plagiarism detection tools can assist educators with large classes and limited time, when implemented properly. This is the part that requires buy in from the end user and resources from the institution to get the faculty up and running (6). While powerful, these can be cumbersome and often lack the features that instructors and students who are digitally savvy expect. Many publisher digital tools integrate with the University LMS’s and are adopted in conjunction with, or more frequently now instead of a printed textbook. McGraw Hill’s Connect and LearnSmart platforms have been optimized for their e-textbooks and integrate with most LMS’s (7). Other purpose-built digital tools are coming online that add features that students expect like Bring Your Own Device applications; Top Hat is one of these platforms that can be used with mobile devices in and out of the classroom (8).
So what has endured?
In my almost 20 years in higher education classrooms and labs, lots of tools have come and gone. What endures are passionate educators making the most of the technology available to them. No technology, whether digital or bench top hardware, will solve a classroom or teaching laboratory problem without the educator. While these various technologies are powerful enhancements to the student experience, they fall flat without the educator implementing them properly. It’s not the tech, it’s how the tech is used that makes the difference, and that boils down to the educator building out the course to match the learning objectives they set.
- Leverage the technology you already have.
- Get fully trained on your LMS and any other digital tools you may already have at your institution. The only investment you will have here is your time and effort.
- Check the cabinets and closets, there is a lot of just out of date equipment lying around that can be repurposed. Perhaps a software update is all you need to put that old gear back in rotation.
- Choose technology that matches your course objectives.
- Small and inexpensive purpose-built tech is becoming readily available, and can be a good way to add some quantitative data to the laboratory experience.
- Top of the line gear may have many advantages for ease of use and reliability, but is not necessarily the best tool to help your students accomplish the learning objectives you set.
- Investigate online options to traditional tools.
- eBooks, OpenStax, and publisher’s online tools can be used by students for a lot less money than traditional texts and in some cases these resources are free.
|Wes Colgan III is the Education Project Manager for ADInstruments North America. He works with educators from all over the world to develop laboratory exercises for the life sciences. He conducts software and hardware workshops across North America, training educators to use the latest tools for data acquisition and analysis. He also teaches the acquisition and analysis portion of the Crawdad/CrawFly courses with the Crawdad group at Cornell. He has been a Faculty for Undergraduate Neuroscience member since 2007, and was named educator of the year for 2014. Prior to Joining ADInstruments, he was an assistant professor at Louisiana Tech University where he was in charge of the introductory biology lab course series.|