Chris Jones Moravian College

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Genomics at Moravian College

Course Overview

Here is the catalog blurb for the course:


This course explores the techniques used to sequence and assemble whole genomes and to analyze the results at the gene and genome levels; it is extensively computer-based. By the end of the semester, each student will have improved the sequence quality of 40,000 base-pairs of DNA to a publishable level and extensively annotated it, indicating the locations of genes, repeat sequences, and other sequence motifs.


Prerequisites: BIO210 (Genetics); permission of the instructor is required as well. This course counts toward the major and minor in Biology and in Biochemistry as as upper-level elective course.


Implementation


I am currently teaching this course for the fourth time. In the spring of 2007 I had 5 students (2 sophomores and 1 junior who had just finished my sophomore genetics course the previous semester, along with 2 seniors) along with a very talented junior who was my TA (I've never had a TA since, not because the student wasn't good -- she was one of the best students I've ever had -- but as I only teach the course in alternate spring semesters, only sophomores would still be around for the next iteration, and I don't usually allow them to take the course). In the spring of 2009 I had 6 students (3 juniors, 3 seniors), in spring 2011 I had 5 students (3 juniors, 2 seniors), and this year I have 8 students (2 sophomores, 2 juniors, 4 seniors). Moravian is a small liberal arts college (about 1400 FTE students currently), so 5 to 8 students is not too surprising for a "scary" upper-level elective course.


We do both finishing and annotation in a 14-week semester, meeting 6 hours per week. We have 3-hour lab blocks every weekday afternoon at Moravian, so I simply schedule the course for the Tuesday and Thursday blocks. I originally wanted to schedule a 7th hour, but it proved problematic fitting into everyone's schedule; given how few students I had, I couldn't afford to jettison anyone so I abandoned that 7th hour. I usually run the course in our Mac computer lab, which lends itself to a fairly informal approach; this has worked well for me.


The first time I taught the course, I modeled my syllabus very heavily (to put it kindly) on what Sally et al. have done for the Bio4342 course at WashU. This was a mistake, but that's how we learn, right? My students did well, and learned quite a bit, but I found myself scrambling constantly to bend and edit the course materials to fit their background knowledge. In retrospect I would have been better off doing more of the legwork myself, so that I would have been more comfortable with the material I was presenting. It would have taken more time, but I think I would have been happier with my version of the course that way. In the second go-round we had a lot of technical problems implementing the Live-CD approach, which I used in an attempt to avoid problems asking our IT people to install "foreign" programs on the computers in just one lab (We're a small school, and the IT folks on the ground are absolutely great, but it's a question of Official Policy, you understand....) The third time was mostly charmed — technical problems were minimal and I think I managed a good balance of background lecture/discussion and hands-on work on projects. This semester there have been a few more technical glitches, but the students are taking it in stride -- nothing like shared inconvenience to help the bonding process.


I chose not to assign a textbook for the course the first time. I think that it would have been better if I had, but I couldn't find one that seemed to fit the content of the course very well, and I didn't anticipate using a book much for class directly, so I decided against it (I try very hard not to be one of those faculty who force students to buy hideously expensive textbooks and then not use them for the class). I did assign a significant number (12 or so) articles from the primary literature for class discussions. In 2009 I assigned Brown's Genomes as a text, but ended up not using it much in class, largely because the aforementioned technical issues ate so deeply into class time that I didn't want to sacrifice more hands-on time to the text. Which resulted in exactly the sort of situation I try to avoid, assigning an expensive book and not using it enough to justify the cost -- which one student dinged me for (rather hard) on his course evaluation. Fair enough. My lesson? I need to make sure that the tech end is rock-solid and bolted down far in advance so that I can focus on pedagogy and process. The third time I again chose not to assign a textbook, and I think that was okay, this semester we're using Lesk's Introduction to Genomics, and I'm managing the balance between text and computer work well, I think.


According to the student course evaluations, the open class structure was good, but more time in class would have been helpful. (Yes, students wanted *more* class time -- go figure!). They also appreciated gaining increased comfort with/comprehension of the primary literature (we read genomics papers over the course of the semester, the number varying from year to year), and the presence of the TA was very helpful, although the students havent' had that luxury since the first year of the course. I've got two very good sophomores this year, though, so maybe in 2015....


Syllabus for BIO391 (Genomics)


Week 1 = background (research problem, review sequencing chemistry, gene structure); watch Virtual Tour of GSC; discuss large-scale cloning/sequencing strategies


Week 2 = overview of finishing process; intro to Consed/Phred/Phrap


Week 3 = discuss genome structure (repetitive elements, gene density, synteny)


Week 4 = begin working on fosmids; discuss chromatin structure and effects on gene expression


Week 5 = fosmid finishing


Week 6 = fosmid finishing; describe restriction digestion (to put the in silico digests in context)


Week 7 = fosmid finishing


[spring break]


Week 8 = finishing presentations; discuss gene finding (homology, BLAST, synteny, ESTs)


Week 9 = introduction to UCSC browser, FlyBase; begin annotating fosmids


Week 10 = continue annotating fosmids


Week 11 = continue annotating fosmids; discuss multiple sequence alignments and Clustal


Week 12 = continue annotating fosmids; discuss sequence repeats and RepeatMasker


Week 13 = finish annotating fosmids


Week 14 = annotation presentations


Grading

The grades for the class were based on a number of components:


participation in discussion of readings = 100 points

problem sets (homework) = 100 points

written report on finishing fosmid clone = 100 points

oral report on finishing fosmid clone = 100 points

evaluations of peer finishing reports = 100 points

oral report on annotation of fosmid clone = 100 points

written report on annotation of fosmid clone = 100 points

evaluations of peer annotation reports = 100 points


In addition, I gave students another 100 points to distribute as they wished among the oral and written reports (before the first one was due, of course), so that they could play to their strengths in oral or written presentations.