Adam Haberman Oberlin College

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Genomics at Oberlin College

Course Overview

BIOL336 was designed as a lecture for up to 16 students with a mandatory lab.  There are 2 lab sections with up to 8 students in each.  In the lecture course, students learn about many aspects of modern genomic techniques, including sequencing techniques, gene mapping, comparative genomics, analysis of variation within species, transcriptome and proteome analysis, and metagenomics.  In the lab, students participate in the full GEP program of sequence improvement and annotation.  Labs meet for 3 hrs a week, and students are informed that they will likely need to spend up to 3 more hours each week to complete their projects.



Implementation

Lessons Learned and Future Plans

I have taught this course twice, and feel that there are strengths and weaknesses to coupling GEP activities with an independent lecture course.  While the lecture covers the concepts that students work with in the GEP, a majority of lecture topics are not connected to the lab activities.  This is not unusual in science classes, but it does mean that GEP lab activities are often disconnected from the material being covered in lecture. 


On the other hand, I have ample opportunity to prepare students before they begin their annotation project in the second half of the semester.  We spend a week of lecture discussing sequence alignments, including blot plots, the Smith-Waterman algorithm, and the mechanics of BLAST searching (including HSPs).  We also discuss the UCSC browser and use it multiple times during the semester.  This training (including homework problems and test questions) allows students to get moving quickly on their Annotation projects.  This year, many of my students took red-level annotation projects and finished them ahead of schedule.


I have had some difficulty finding the correct level of projects for my students.  The first time I taught this course (Spring 2012), I chose all green finishing projects, just to be sure I could manage everything.  These projects were finished too easily, and the students were not fully engaged in the work.  I ended up creating a walkthrough of a red project, which the students did during lab period after they had all finished their projects and had nothing else to do.  In the Spring of 2013, I wanted to give the students yellow finishing projects, but few of these were available.  I ended up using red projects, which were often too daunting.  Again I had problems with engagement, but now because students felt overwhelmed.  I suspect that my inexperience with these types of challenging projects did not help.  Strangely, I also had a lot of resistance to the format of Consed this year, which I did not have the first time.

For annotation projects, I allowed students to choose the level of difficulty that they wanted, which I feel helped the students take more ownership of their projects from the beginning.  In 2012, I let students do green projects as originally planned, or take more challenging yellow projects.  If they chose the harder project, their project grade would count for a larger percentage of their final grade and their worst exam would count for a smaller percentage.  Most students chose yellow projects.  Interestingly, the two honors students in the class chose green projects because they felt overwhelmed with the process of finishing their projects and writing their theses.  In 2013 I gave a similar choice, but now students could choose only between yellow and red projects.  Engagement in these projects was high, and I would continue to offer this choice in the future.

Syllabus for

BIOL 336: GENOMICS
Genomics, the study of all the DNA of an organism, is revolutionizing biological research. As DNA sequencing becomes faster and cheaper, genomic techniques will become widespread in research, medicine, and elsewhere. In this class, we will explore the techniques of genomics and see what kind of information we can learn once we have sequenced an organism’s genome. In lab, we will participate in primary research to sequence and analyze genome data.
OBJECTIVES:
• Understand how a genome is sequenced and analyzed.
• Learn how and why genomics is used in different fields.
• Analyze multiple lines of raw data to understand a genome sequence in detail.
INSTRUCTOR: Prof. Adam Haberman
PREREQUISITE: BIOL 213
CLASS HOURS AND LOCATION: Lecture - MWF 11:00-11:50 in A155. Lab – M or T 1:30-4:20 in A262 (Occasionally in the Science Library computer lab N181).
OFFICE HOURS: W 1:30-2:30, Th 10:00-12:00, or by appointment in K231. I can always be reached by email at adam.haberman@oberlin.edu.
TEXTBOOK: A Primer of Genome Science, 3rd Edition by Gibson and Muse
CLASS FORMAT
Topics to be discussed in lecture are listed below. This schedule is subject to change as needed. Some lecture periods will be devoted to discussion of laboratory research projects.

Week Topics Reading Assignments
Feb 6-10 Introduction to Genomics, Molecular Biology review, Genome sequencing 1-4, 65-94
Feb 13-17 Gene mapping, Comparative Genomics, Web resources, Genome projects 4-27 Lab - Hwk 1 due
Feb 20-24 Genome projects, Your research projects Paper discussion 1 - Feb 22 28-58 Feb 22 - Paper analysis 1 due Feb 24 - Hwk 2 due
Feb 27-Mar 2 Bioinformatics 113-128
Mar 5-7 Genome variation No class March 9 133-146 Mar 7 - Hwk 3 due
Mar 12-16 Analysis of Single Nucleotide Polymorphisms (SNPs) 146-152, 158-186
Mar 19-23 Your research projects Exam 1 - Mar 21 --- April 2 - Finishing report due
April 2-6 Features of genome sequences, Annotation of genes, Gene expression analysis 95-113
April 9-13 Gene expression analysis 191-252 Lab - Hwk 4 due
April 16-20 Gene expression analysis, Proteomics Paper discussion 2 - April 18 259-285 April 16 - Hwk 5 due April 18 - Paper analysis 2 due
April 23-27 Proteomics Paper discussion 3 - April 27 April 27 - Paper analysis 3 due
April 30-May 4 Metagenomics, Metabolomics, In silico genomics 59-60, 325-342
May 7-11 Systems biology, Your research projects Exam 2 - May 7 May 17, 9 PM - Annotation report due

PAPER ANALYSIS: At three points during the semester, we will discuss primary research articles as a class. You will be given these articles a week in advance. You are expected to read these articles in advance of the class discussion. To guide your reading, you will be assigned Paper Analysis questions. These short answer questions must be turned in on the class Blackboard site before the start of class on the day of the paper discussion.

HOMEWORK ASSIGNMENTS: There will be several homework assignments throughout the semester. In general, you will receive the assignments a week before they are due. The purpose of these assignments is to have you practice using the tools we have discussed in class. They will significantly aid you in mastering the material. Homework assignments must be turned in on the class Blackboard site before the start of class on the due date.

GENOMES IN THE NEWS: Every Friday, the last 10 minutes of lecture will be dedicated to the discussion of popular news articles related to genomics. I will bring some items we can discuss, but the floor will be open for any items brought by the class. We can discuss articles about the uses of genomics, ethical controversies, misconceptions, or anything else of interest. Articles do not need to be cleared in advance and presentations will be informal.

LABORATORY PROJECTS: Students will perform two research projects during the semester. For the first half of the semester, we will perform sequence improvement or finishing. For the second half, we will annotate genome sequence. These are primary research projects performed as part of the Genomics Education Partnership (GEP). We will use several resources generated by GEP in these projects. The projects are original research projects. Each Oberlin student will analyze a different genome region. Each region will be independently analyzed by a student at another institution. The two analyses will then be reconciled by other students at Washington University in St. Louis. Once enough data has been compiled and verified, it will be published as original research articles. Students will be eligible to be authors on these papers if they complete their analyses and read a draft of the paper before publication. In order to complete these requirements, it is important that I am able to reach you by email for 2-3 years after completion of the course. If I cannot give you a draft of the paper to read, you will not be listed as an author.

Lab projects will be graded on a contract basis, meaning that if you complete the assigned tasks you will get full credit. Details of the work to be performed will be discussed in class, but your general responsibilities are:
1. Analyze your assigned sequences to the best of your ability.
2. Keep detailed notes about the reasoning behind your analysis.
3. Report your analysis and underlying reasoning clearly and in the format requested.
Lab work will be performed in public computer labs. Therefore, you will need to save a copy of your work at the end of every session. Oberlin StuLocker has more than enough storage space for our needs, but you are free to use any other system you wish, including Dropbox or a flash drive. In addition, I will copy every person’s work onto a portable hard drive at the end of each lab period.
GRADES
Grades will be assigned for the following activities:
Exam 1 ------------------------------------------------------------- 20%
Exam 2 ------------------------------------------------------------- 20%
Sequence Improvement project ----------------------------- 20%
Annotation project ----------------------------------------------- 20%
Homework and Paper analysis assignments ----------- 20%
CLASS POLICIES
HONOR CODE: This class will, of course, adhere to the guidelines of the honor code. You will need to include a statement of your adherence to the honor code with each assignment that is turned in. Note that, because each research project will analyze different DNA sequences, working together on research projects will not violate the honor code.

LATE ASSIGNMENTS: Homework and Paper analysis assignments should be turned in on Blackboard by the start of class on the due date. Late assignments will lose 10% of total possible credit for each 24 hour period they are late.

CELL PHONES: Please turn off or turn to silent all cell phones, tablets, computers, and other noisemakers during class, as a show of respect to your classmates.
STUDENTS WITH DISABILITIES: Students with special needs due to learning disabilities, medical conditions, or other factors are encouraged to discuss those needs with me early in the semester.
LAB SECTION ASSIGNMENT: The size of each lab section was capped at eight students to ensure a student:teacher ratio in which all students would get the attention they required. Therefore, it is not acceptable to attend a section other than your assigned section. It may be possible to assign you to a different section at the beginning of the semester, as long as space exists on the roster or someone else is willing to make a complementary switch.