Ken Saville - Albion College

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My experience with the GEP course:

Biology 389:  genomics

Below is a general description of the course I taught at Albion.  To see the syllabus click here Saville's syllabus

I taught genomics as a stand-alone course at Albion College in the spring of 2008. There were a total of 10 students, including eight seniors and two juniors. One student had participated in the TA training at Wash U. She took the course for credit, working on her own project and helping with course logistics and with other students’ projects. Because the course was taught in addition to my normal load, the schedule was somewhat irregular. We met for one hour on Tuesdays and four hours on Thursdays. This wasn’t an ideal schedule, but overall it worked out fine.

Because we don’t have access to Macintosh computers, we used the Linux operating system to run the finishing program consed. To do this we loaded a virtual machine using VMware onto 12 PC laptop computers. Because I was completely unfamiliar with Linux or Unix going into this project, we ran into a number of computer-based problems along the way. Primarily these problems were due to incomplete installation of the programs consed, phred and phrap. However, with considerable help from the IT staff and computer science colleagues at Albion, and of course from Chris Schaeffer and Wilson Leung at Wash U. we were able to complete several finishing projects. However, this took much longer than intended and limited the amount of time we could spend on annotation.

Overall, I consider this to be an ideal course from both the perspective of the faculty member and the students. Faculty are often confronted with a conflict between how much content to include in a course versus how much focus should be placed on the process of learning. This course allowed me to focus mostly on the process of learning new material.  That is, with the exception of some of the scientific background, we learned what we needed as we needed it. Students often yearn for a clear connection between what they are studying and why it is important. This course allowed students to tap into knowledge from previous courses and to integrate this knowledge with new analytical skills to solve a real problem.

The atmosphere of the class was that of a problem solving team, reminiscent of a small research group, start-up company, or other similarly dynamic and creative group.  This was truly a collaborative effort between the students and the professor.  Rather than a simple didactic dispensation of information, the roles of the professor included those of facilitator, technical support, behind-the-scenes problem solver and, perhaps most importantly, a co-learner of the tools and skills involved in solving problems. In fact there were many instances where the professor relied completely on students who had solved a particular problem to teach other students how to solve similar problems.  It  While two longer class sessions per week would be a better structure for the course, we used the one hour session to discuss the underlying biology of the DNA sequencing problem being addressed. It also often served as a ‘problem identification’ day, with the intervening day used by the professor to fix any computer issues and the following session being used to solve the problems identified. This process of just identifying and clearly describing a problem, separate from trying to actually solve the problem, was an excellent learning experience. The students, while often impatient and anxious to know the answer, got an excellent sense of how the problem solving process actually works. Specifically, that problem solving occurs in steps: Identify the problem, suggest various causes of the problem, attempt appropriate solutions to the problem, repeat as necessary, seek outside help when needed.

At the end of the semester the entire class prepared and presented a poster at our annual undergraduate research symposium. This process was also an excellent learning experience. Certain students stepped up as leaders of the process, gathered information from others in the class and collated this information into a poster. All students were present at the poster session.  

In conclusion, this course had all the hallmarks of a ‘capstone experience,’ in which students integrate past knowledge with new skills and information to solve a real-life problem.

The students were very enthusiastic about this course, beginning the semester before the course was offered. They really embraced the concept and the process. It was clear that they enjoyed working on something that was new and didn’t involve extensive review of basic concepts they had learned in other classes. They also benefited from the sense of teamwork, shared responsibility and shared accomplishment throughout the semester. They all were also thrilled about the potential to be co-authors on a research publication, and enjoyed the opportunity to present their research to the campus community. Many of these students will be attending graduate school or medical school and will benefit greatly from the experiences from this course

Here's a link to the poster presented by my students at the Spring 2008 Elkin Isaac Undergraduate Research Symposium at Albion College.  If you want a copy of it and you have trouble downloading it from here let me know ( and I'll send it to you.

genomics poster

Biology 317 genetics.

This class typically has 30-38 students, divided into two lab sections.  We do annotation as part of the lab component.  We usually use some of the online course material from GEP, including the 'simple annotation problem', then practice an anotation problem selected from the 'sandbox' portion of the gep web site.  Finally each pair of students is given one or two genes to annotate, and the final reports are compiled into a report for submission by the instructor.