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Table of contents
  1. 1. Teaching Responsibilities

Teaching Responsibilities

Below are the teaching responsibilities I have had over the last four years.


Number of Students

Year Taught

Biology of Microorganisms Laboratory


2008, 2009, 2010

Biology of Microorganisms Lecture


2008, 2009, 2010, 2011

Food Microbiology Laboratory


2008, 2011

Microbial Physiology Laboratory



Microbial Diversity Research Laboratory


2009, 2011, 2012


Student Learning Challenge or Problem


As part of our advanced microbiology laboratory, students generate millions of base pairs of DNA sequencing from a pyrosequencing protocol using a GS Junior. Several sessions are then devoted to cleaning up this data and then analyzing it using bioinfomatics tools. We have used a hands on approach where the students are guided step-by-step through the analysis process, until the desired analytic outcomes are reached. Formal assessment after the bioinfomatics sessions has shown that students are obtaining, at best, a rudimentary knowledge of how to use these tools and what they are actually doing. At worst, they gain no understanding, or appreciation of bioinfomatics, except that it is powerful and complex. The difficulty students have with bioinfomatic analysis is understandable since it requires a skill set that many of them have not developed; using a command-line interface, computer programming in perl, being familiar with available unix tools, and being able to manage large data sets.

In a study by Lim et al. (1) bioinfomatics was taught using problem-based learning (PBL) and e-learning tools. PBL topics in bioinfomatics were guided by LAMS software (2), an e-learning environment developed by LAM international. An advantage of this approach was the ability of the students to proceed through the lesson at their own pace, only moving on when they were confident they understood the concepts being taught. The information reported in this study focused on student reaction to the technique, and not their formal assessment of learning. Students overall had a positive response to PBL, but a negative response to the LAMS technology, with only one-third indicating that they would be upset if LAMS was removed from the curriculum. Another drawback of the LAMS system, was its cost, with a license for 1 year being over $3000. In addition, the curriculum is then dependent on a commercial software company whose business model, or very existence, may diverge from your teaching goals. The study also showed that students were at best, luke-warm to the use of technology.

I would like to explore using PBL in combination with the development of open source tools to help build a bridge to a firm foundation in understanding bioinfomatics tools and knowing how to use them effectively. The e-learning part of this approach would be delivered by a moodle plug-in specifically developed to facilitate PBL. Moodle ( is an open source software package designed for the production of internet-based courses. It has a very active user and development community. I also have extensive experience is writing modules for php content systems such as moodle and would be able to extend the PBL module in moodle to my needs.

 Professional Development Goals

I have taught at the university for over 2 decades and have developed many courses over the years. In my first 10 years of teaching I had earned high marks on my evaluations in the teaching laboratories and in the introductory lecture course I taught in the summer. However, I was always frustrated by the lack of engagement with the students in the lectures when compared the teaching laboratories. I felt there had to be a better way. Every year I would I tried new methods and each year it would get a little better. Two events changed everything.

First, in 2006 I had the great fortune to be asked to participate in a redesign of our introductory microbiology course for majors. That process exposed me to a completely different world view on how to develop, organize, present and assess learning in a classroom. It then inspired me to apply many of the techniques I learned in that workshop to my own teaching including backward design, think-pair-share, one-minute papers, concept maps, clicker questions, and many more. Second, Professor Gary Roberts helped me to hone my development of clicker questions so that they were not just asking for regurgitation, but were challenging and engaging the student in the material we were studying. Gary was generous enough to work with me on questions and come to my classroom and evaluate the success of what I was doing. I am a far more effective teacher because of these experience and its application to my teaching. Qualitative reactions from students and their performance on tests has suggested that these methods work. My lecture classes are now just as engaging as the laboratories.

In the past few years I have begun to extend these methods in novel ways. For example, using a wiki to encourage collaboration between students in an independent research class. As I have begun to create new approaches, the desire to quantitatively access their effectiveness has become a more pressing issue. My present goal is to learn the common practices for probing the effectiveness of teaching techniques and when to apply them.

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