How I used the principles of software carpentry to teach a class on Epidemiology and Evidence based health

  1. The students were provided a set of questions.
  2. For each question, the students were asked to select five primary studies that would address the outcome in the question. For example, a question might be “What is the effectiveness of Nicotine replacement therapy for smoking cessation?”
  3. The students would identify an outcome of their choice and five primary studies that would best address that outcome and appraise the evidence presented in these articles for that outcome and intervention pair.
  4. The students would use the GRADE approach and use GRADEPro webapp to abstract information from the studies, appraise the level of evidence presented in the studies and would construct an evidence portfolio and a summary of findings for the studies combined.
  5. Construction of this evidence portfolio would involve that the students would have to construct a summary of findings based on the effect estimate and effect size, the 95% confidence interval band, and depending on the type of effect estimate (absolute effect or relative risk), comment on the use of each effect estimate in terms of their magnitude, the quality of the evidence (experimental studies would be awarded a higher grade of evidence than observational epidemiological studies). This process would take about two hours for a body of five primary studies and the process would involve understanding of the study designs but also that hte students would be facile working with the GRADEPro programme.
  1. The students would complain that the webapp GRADEPro was not easy to work with and was a bloated software as it would take several minutes to hours to boot up and store data locally, and it was not very intuitive to understand if they were left to themselves to work with it.
  2. While the students seem to understand how to do the critical appraisal using GRADEPro during demonstration and I even used a webinar I conducted with an international agency to supplement my teaching materials, yet, when it came to provide feedbacks on this module, the students would complain that it was tedious and the quality of the final output of their work was not very satisfactory. I was confused. Some students seemed to understand the theory well, but when it came to produce the results, the results were poor. Most students would get a B or lower grade in this assignment and that was perhaps due to their unfamiliarity with the software. Many students had also problems interpreting data results from individual articles they would select, and this also added to the complexity.
  3. Third, students would set up appointments with me so that I would have to go one on one training with the students to use this tool. This used up considerable time for me, and I frequently found several students would wait outside my room and I had to work several hours with the students teaching them how to work with the tool and how to conduct critical appraisal using GRADEpro, despite showing them in the class and sharing teaching and study materials.
  4. Several students would ask for extension and report that they were unsure as to how to work with the assignment and use Gradepro despite several rounds of working with them. Several of them reported assignment anxiety.
  1. A short two-day intense programme of hands-on teaching would be preferable to five day or longer workshop format of teaching. This two day teaching would be workshop format anyway.
  2. The purpose would be to teach computational thinking rather than the nitty gritty of working with programming languages or BASH scripting or Python or R (these were all open source software that would run in any operating system).
  3. The instructor and the students would work together at the same time on the same problem or the same programming challenge; this would slow down the instructor. This mode of teaching was referred to as “live coding”. Live coding not only slowed down the instructor but it also made the teaching more interactive. More importantly, the students would learn from the mistakes even the instructor could make.
  4. Such a mode of teaching would encourage the students to help each other and form peer teachings; for example, if the students were to work in pairs using a single computer, then one student could help another student as they worked on the problem and would take turns.
  5. A system of repeated feedbacks were introduced. At each gap, the students were encouraged to leave feedbacks and their learning needs for the subsequent session. This enabled the instructor to tailor instructions.
  6. At different points in the lecture or instruction or working with the students, the instructor would stop and check the level of understanding of the students. This provided an opportunity for the instructor to assess how much of the instruction got transmitted.
  1. I changed the seating of the students from a more “stadium style seating” to a more “dinner table style seating”; now the students sat around a table
  2. Each student was asked to bring a computer (not a tablet or a chromebook, although this would work on a tablet or a chromebook). If a student did not have a computer, one would be arranged for the student as a loan laptop borrowed from the IT department.
  3. A problem was distributed to the students and detailed instructions on how to use GRADEPro and the GRADE approach readings were distributed a week in advance to the students. They were expected to read this before coming to the class. In this practice, it was similar to what was done in the previous years.
  4. I would work with the students on the same problem.
  5. Each student was provided with a red and a green sticky note or post it note. If the student completed the task assigned to him or her during the interactive session, the student would stick the note on the back of their laptop screen (or the lid); if the student was stuck for some reason or did not progress or could not understand, then the student would stick a red sticky note on the back of the computer. I would then troubleshoot. This was done as I did not have a teaching assistant with me in the class.
  6. From time to time, I would explain a key topic and ask a question. The students raised their hands and answered the questions. However, it was different from a typical software carpentry session in the sense that in a software carpentry workshop, we use a webpage or etherpad; in our case, we just used ora question and answers.




Professor @ University of Canterbury, Doctor, scholar, data scientist, Cantabrian. ENS: arinbasu.eth & mastodon instance:

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Arindam Basu

Arindam Basu

Professor @ University of Canterbury, Doctor, scholar, data scientist, Cantabrian. ENS: arinbasu.eth & mastodon instance:

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