Inimary Toby-Ogundeji, PhD Assistant Professor 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:
Perform summary statistics
Workflow Step-by-Step instructions and screenshots from JupyterLab
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.
Diane H. Munzenmaier, PhD Program Director Milwaukee School of Engineering
For most of my career, I taught physiology and genetics to medical students and graduate students. My experiences with many students who had difficulty succeeding in these courses led me to the realization that the way high school and college students learn the biological sciences does not translate to effective physiology learning and understanding at the graduate level.
Medical students, by virtue of their admission to medical school, have, by definition, been successful academically prior to matriculation and have scored well on standardized exams. They are among the best and brightest that our education system has to offer. Yet, I have always been amazed at how many medical students truly struggle with physiology. It is considered by many students to be the most difficult discipline of the basic medical sciences. Most students come into medical school as expert memorizers but few have the capacity or motivation to learn a discipline that requires integration, pattern recognition, and understanding of complex mechanisms. My overall conclusion is that high school and college level biological science education does not prepare students to succeed in learning physiology at the graduate level. Furthermore, I believe if students were prepared to better appreciate and excel in basic physiology at earlier grade levels, the pipeline for graduate education in the physiological sciences would be significantly increased.
Over the past 5 years, it has become a passion of mine to promote a new way of teaching biology and physiology: one that helps students make connections and that lays a conceptual framework that can be enhanced and enriched throughout their educational careers, rather than one that promotes memorization of random facts that are never connected nor retained. I recently joined the Center for Biomolecular Modeling at the Milwaukee School of Engineering (MSOE CBM) in order to focus on developing materials and activities to promote that type of learning and to provide professional development for K-16 teachers to help them incorporate this type of learning into their classrooms.
One of my first projects was to develop resources to allow students to study the structure-function relationships of a specific protein important in physiology and use that understanding to relate it to relevant physiology/pathophysiology concepts. The program is called “Modeling A Protein Story” (MAPS) and, so far, I have developed resources for 3 different project themes: aquaporins, globins, and insulin.
The overall concept is for the students to build their understanding slowly and incrementally over time, usually as part of an extracurricular club. They start by understanding water and its unique properties. Then they learn about proteins and how they are synthesized and fold into specific 3D conformations in an aqueous environment based largely on their constituent amino acids and how they interact with water. Eventually they progress to learning about the unique structure of their protein of interest and how it is related to its function. Once they have developed a solid understanding of that protein, they work in teams to choose a specific protein story that they will develop and model. This includes finding a structure in the Protein Data Bank, reading the associated research paper to determine what was learned from the structure, designing a model of the structure in Jmol, an online 3D visualization software, and 3D printing a physical model of the protein that helps them tell their story. Stories can be anything related to the theme that the students find in their research and consider interesting. For example, student-developed aquaporin stories have ranged from AQP2 in the kidney to AQP4 in the brain to the use of AQP proteins to develop biomimetic membranes for water purification in developing countries. By choosing projects that students are interested in, they more readily accept the challenge of reading primary research literature and trying to piece together a confusing puzzle into an understandable “story”.
In the past year, I have used the insulin theme resources and piloted an active learning project-based curriculum at the undergraduate, high school, and middle school levels on insulin structure-function, glucose homeostasis, and diabetes mellitus. The type of learning environment in which this curriculum was introduced has varied. Middle school level children participated in the active learning environment as part of a 2-week summer camp. High school students from an innovative charter school in downtown Milwaukee were introduced to the project-based curriculum as a 9-week seminar course, and the activity was taught to freshman biomolecular engineering students at the Milwaukee School of Engineering as a team project in their first quarter introductory course.
Some of the activities utilized materials that we have developed at the MSOE CBM and were subsequently produced for distribution by our sister company, 3D Molecular Designs. Others utilize resources that are readily available online such as those available at the Protein Data Bank at their educational site, PDB-101. Finally, still other resources have been developed by us specifically for this curriculum in order to help the students move between foundational concepts in an attempt to help them make important connections and to assist them in developing their conceptual framework.
One of the activities that helps them try to make sense of the connection between glucose and insulin is this “cellular landscape” painting by Dr. David Goodsell at Scripps Research Institute and available at PDB-101.
They learn the basic concept that when blood glucose increases after a meal, insulin is released from the pancreas and allows glucose to be taken up and stored by the cells. But how? When they are given this landscape and minimal instructions, they must look closely, connect it to what they already know and try to make sense of it. They work together in a small group and are encouraged to ask questions. Is this a cell? If so, where is the plasma membrane and the extracellular/intracellular spaces? What types of shapes do they see in those spaces? What is in the membrane? What are those white dots? Why is one dot in one of the shapes in the membrane? Why are there yellow blobs on the outside of the cell but not on the inside? Eventually they piece together the puzzle of insulin binding to its receptor, leading to trafficking of vesicles contain glucose transporter proteins to the plasma membrane, thereby allowing the influx of glucose into the cell. By struggling to make detailed observations and connections, a story has been constructed by the students as a logical mechanism they can visualize which is retained much more effectively than if it had been merely memorized.
In other activities they learn how insulin in synthesized, processed, folded, stored, and released by the pancreatic beta cells in response to elevated blood glucose. They use a kit developed by MSOE CBM that helps them model the process using plastic “toobers” to develop an understanding of how insulin structure is related to its function in regards to the shape and flexibility required for receptor binding but also related to its compact storage in the pancreas as hexamers and the importance of disulfide bonds in stabilizing monomers during secretion and circulation in the blood.
As the students build their understanding and progress to developing their own “story”, the depth of that story depends on grade level and the amount of time devoted to the project. Undergraduate students and high school students who have weeks and months to research and develop their story tend to gravitate to current research into protein engineering of insulin analogs that are either rapid-acting or slow-release, developed as type 1 and type 2 diabetes medications, respectively. The basic concepts behind most of these analogs are based on the structure-function relationships of hexamer formation. Rapid-acting medications usually include amino acid modifications that disrupt dimer and hexamer formation. Slow-release medications tend to promote hexamer stability. Middle school students or high school students with limited time to spend on the project may only focus on the basic properties of insulin itself. The curriculum is driven by the students, so it is extremely flexible based on their capabilities, time, and motivation. Students ultimately use their understanding of insulin structure-function to design and 3D-print a physical model that they highlight to show relevant amino acid modifications and other details that will help them to present the story they have developed based on their learning progression and research.
In conclusion, we have found that this type of open-ended project-based active learning increases learning, retention, and motivation at every educational level with which we have worked. Students are initially frustrated in the process because they are not given “the answer” but they eventually learn to be more present, make observations, ask questions, and make connections. Our hope is that introduction of this type of inquiry-based instruction in K-16 biological sciences education will eventually make the transition to graduate level physiology learning more successful.
Diane Munzenmaier received her PhD in Physiology studying the role of the renin-angiotensin system on skeletal muscle angiogenesis. This was followed by postdoctoral study of the role of astrocytes in stroke-induced cerebral angiogenesis. She joined the faculty of the Department of Physiology at the Medical College of Wisconsin in 1999 and the Human and Molecular Genetics Center in 2008. As Director of Education in the HMGC, Dr. Munzenmaier lectured and developed curriculum for medical and graduate school physiology and genetics courses. She developed an ACGME-accredited medical residency curriculum and Continuing Medical Education (CME) courses for physician education. She also enjoyed performing educational outreach to K-12 classrooms and the lay public. She is passionate about education and career mentoring for students of all levels. Her specific interests in biomedical science education are finding engaging ways to help clarify the link between structure and (dys)function in health and disease.
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
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
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.
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.
What has to shift to change your perspective? Thomas Kuhn coined the term paradigm shift and argued that science doesn’t progress by a linear method of gathering new knowledge, rather, a shift takes place when an anomaly subverts the normal practice, ideas and theories of science. Students learn through interaction with the surrounding environment mediated by prior knowledge from new and previous interactions with family, friends, teachers, and other sociocultural experiences (Falk & Adelman, 2003). Deep understanding of concepts depend on the interaction of prior experience with new information. As Kuhn stated in his 1962 book The Structure of Scientific Revolutions, “The challenge is not to uncover the unknown, but to obtain the known.”
In order to assess what students know, you need to find out what they already knew. An assessment can only provide useful information if it is measuring what it is intended to. In the medical field, assessments are used all the time, for example, an MRI is a useful diagnostic tool to determine the extent of tissue damage but it is not necessarily useful for establishing overall health status of an individual. Assessing what a student knows with a multiple choice test may also not be useful in establishing an overall picture of what knowledge a student possesses or how that knowledge is applied, especially if the items are not measuring what they are supposed to. Construct validity provides evidence that a test is measuring the construct it is intended to. How to measure construct validity is beyond the scope of this article, for information, see the classic work by Messick (1995). Outside of the psychometrics involved in item or assessment construction, I’ll provide some quick tips and techniques I have found useful in my teaching practice. What can you do to separate real learning with deep understanding from good test taking skills or reading ability? How can you assess what students know simply and effectively?
Instruction in a classroom environment needs to be connected with assessment rather than viewing instruction and assessment as separate activities. Understanding student thinking can be done with formative assessment which benefits students by identifying strengths and weaknesses and gives instructors immediate feedback regarding where students are struggling so that issues can be addressed immediately. By providing students with context in the form of a learning goal at the start of a class, the clear objective of the lesson allows them to begin making connections between what they already know and new information. When designing or preparing for a class, ask yourself:
What do I assume they already know?
What questions can I ask that will help me confirm my assumptions?
What are the most common misconceptions related to the topic?
Tips for checking students background knowledge
On a whiteboard or in a presentation, begin with one to three open ended questions and/or multiple choice questions. Ask students to respond in two to three sentences, or circle a response. It’s important to let them know that the question(s) are not being graded, rather, you are looking for thoughtful answers that will help guide instructional decisions. Share the results at the start of the next class or with a free tool like Plickers for instant feedback.
Short quizzes or a survey with Qualtrics, Google Forms, or Doodle Poll can be used via Black Board prior to class. Explain that you will track who responded but not what the individual student responded at this point. Share the results and impact on course design with students.
Group work. Using an image, graph, or some type of problem regarding upcoming course content, have students come up with a list of observations or questions regarding the material. Use large sheet paper or sticky notes for them to synthesize comments then review the themes with the class.
Formative assessment is used to measure and provide feedback on a daily or weekly basis. In addition to learning goals communicated to students at the beginning of each class and warm up activities to stimulate thinking about a concept, formative assessment can include comments on assignments, projects or problem sets, asking questions that are intentional towards essential understanding rather than a general, “Are there any questions?” at the end of a lesson. To add closure and summarize the class with the learning goal in mind, provide index cards or ask students to take out a piece of paper and write in a couple of sentences what the most important points of the lesson were and/or ask them to write what they found most confusing so that it can be addressed in the next class. Formative assessments provide tangible evidence for you to see what your students know and how they are thinking and they provide insight and feedback to students in improving their own learning.
Summative assessment includes quizzes, tests and projects that are graded and used to measure student performance. Creating a well-designed summative assessment involves asking good questions and using rubrics. In designing an assessment that will accurately measure what students know, consider:
What do you want your students to know or be able to do? This can also be used in each lesson as a guiding objective.
Identify where you will address the outcomes in the curriculum.
Measure what they know with your summative assessment.
Based on the measurement, what changes can be made in the course to improve student performance?
Measure what you intend for them to measure.
Allow students to demonstrate what they know.
Discriminate between students who learned what you intended versus those that did not.
Examine what a student can do with what they learned versus what they simply remember.
Revisit learning goals articulated at the beginning of a topic, unit or course.
Use a variety of questions such as multiple choice, short answer and essay questions.
Used for oral presentations, projects, or papers.
Evaluate team work.
Facilitate peer review.
Provide self-assessment to improve learning and performance.
Students do not enter your classroom as a blank slate. Assessing and determining what students know targets gaps in knowledge. By incorporating an activity or a question in a small amount of time at the start and end of a class, you can check on potential and actual misconceptions so that you may target instruction for deep understanding. Background checks of prior knowledge provide awareness of the diversity of your students and their experiences further designing and improving instruction for active, meaningful learning. Creating a bridge between prior knowledge and new material provides a framework for students for a paradigm shift in learning and makes it very clear for them and for you to see what they learned by the end of a lesson or the end of a course.
Falk JH, Adelman, L.M. Investigating the Impact of Prior Knowledge and Interest on Aquarium Visitor Learning. Journal of Research in Science Teaching. 2003;40(2):163-176.
Kuhn TS. The Structure of Scientific Revolutions. 4th ed. Chicago: The University of Chicago Press; 1962.
Messick, S. (1995). Standards of validity and the validity of standards in performance assessment. Educational measurement: Issues and practice,14(4), 5-8.
Jennifer (Jen) Gatz graduated from Ithaca College in 1993 with a BSc in Exercise Science and began working as a clinical exercise physiologist in cardiac and pulmonary rehabilitation. Jen received her MS in Exercise Physiology from Adelphi University in 1999, founded the multisport endurance training company, Jayasports, in 2000, and expanded her practice to include corporate health and wellness for Brookhaven National Laboratory, through 2012. Along the way, Jen took her clinical teaching practice and coaching experience and returned to school to complete a Master of Arts in Teaching Biology with NYS teaching certification from Stony Brook University in 2004. A veteran science teacher for 12 years now at Patchogue-Medford High School in Medford, NY, Jen is currently teaching AP Biology and Independent Science Research. A lifelong learner, Jen returned to Stony Brook University in 2011 and is an advanced PhD candidate in Science Education anticipating the defense of her dissertation in the fall of 2016. Her dissertation research is a melding of a love of physiology and science education focused on understanding connections among cognitive processes, executive functioning, and the relationship to physical fitness, informal science education, and environmental factors that determine attitudes towards and performance in science. In 2015, Jen was a recipient of a Howard Hughes Medical Institute Graduate Research Fellowship.