Genomics at Lock Haven University of Pennsylvania
I developed BIOL323 – Bioinformatics and Genomics as a new course for upper level juniors and seniors in Biology and Biology/Chemistry in 2009/2010. Bioinformatics and Genomics is taught in a computer classroom, where students complete hands-on computer laboratory activities to develop their skills to analyze biological data of a number of types. I developed all of the computer based activities on my own for implementation in Fall 2010. I next taught this class in Fall 2012, as all of our upper-level elective classes offered by our department are offered every other year. I implemented the GEP project as a half semester long research component to this class in Fall 2012 and I plan to do this again in Fall 2014.
This course typically has 16 students who are Biology and Biology/Chemistry majors and they are usually Juniors or Seniors who take the course as an elective. The class meets three hours per week in a computer laboratory classroom. I joined the Genomics Education Partnership in Summer 2012 to provide research experiences for our undergraduates both in this class and in independent study projects.
In Fall 2012, when I first implemented the GEP research project, I divided the students in groups of two or three. Each group annotated one contig of the Drosophila biarmipes dot chromosome with two or three genes, each with a varying number of isoforms. I started the students off with GEP curriculum exercises to practice, and also developed my own assignments during the project to keep students progressing.
I estimate that the time we spent on the GEP project in class was: ~6 weeks x 2 hours per week in class and ~3-4 hours outside of class per week for a total of ~30-50 hours.
Students completely annotated 7 contigs with 2-3 genes each. The students uploaded the annotation data to GEP upon completion at the end of the semester.
Students were surveyed at the end of the semester about their work on this project, and these are the comments that students provided:
• “As much as I struggled with the annotation project, I see it as useful to my education. In lab classes, one is kind of lied to with “cookbook” experiments. I enjoyed having the ability to “fail”. The annotation project gave me something to be proud of.”
• “I learn better through experience. I hate doing pointless “in-the-box” labs. This was worth my time, taught me a lot and has a real, important outcome.”
• “It definitely helped me to learn more patience. But more importantly it put you in a situation where you don’t know the outcome of your experiment which is something you rarely get as an undergrad.”
• “It teaches about the actual research process, especially the challenges of no one else knowing the answer.”
• “It taught me to work independently and forced me to learn what I was doing instead of memorizing.”
• “I had to use time management because this project wasn’t something that could be done in a couple hours the night before it was due.”
• “It gave me hands on experience in the techniques described in lecture which I think is very important.”
• “The annotation project was, by far, the most useful project I have done in my collegiate career. Unlike most other projects, the answers were unknown, and that allowed for the feel of real scientific research.”
Lessons Learned and Future Plans
I found that the course time spent in the computer laboratory with me for students working on this project was not enough when I implemented it in Fall 2012. Students had to work outside of the laboratory on the project, and then did not have my help and quickly became frustrated and overwhelmed, as they commented that they had never worked on a project with was novel with no straightforward answer. The course had three hours of instruction time per week, with a combined lecture/laboratory component, so students ended up spending about 3-4 hours outside of class working on the project on their own. I ended up spending considerable one-on-one time with each student to help them with the project. I surveyed the students at the end of the semester, and 87% suggested that the course be revised to include two additional hours per week of laboratory computer work with supervision by me for help. I am not able to have a Teaching Assistant for this class, so I have to provide the sole source of help for this project.
To this end, I revised the university syllabus for BIOL323, Bioinformatics and Genomics in Fall 2013 to include two hours of lecture and three hours of laboratory per week for 15 weeks (up from just three hours of combined lecture and laboratory per week for 15 weeks), and put the syllabus through our university curricular review. It was approved by the faculty, but denied by the administration because of budgetary issues, so I will again teach the class in Fall 2014 with only three hours of combined lecture/laboratory instruction. I still plan to offer the GEP research experience for my students this fall, but I know that I will be spending considerable time outside of class one-on-one with the students for this project to be successful.
Syllabus for BIOL323 Bioinformatics and Genomics
Instructor: Dr. Carina Endres Howell
Class Times: Tuesday, Thursday 12:30pm-1:45pm (RAUB106)
Office: Ulmer 319
Office Hours: Tuesday 2:30pm -3:30pm, Wednesday 10am -12pm and 2:30pm-3:30pm,
Thursday 10am -11am. By appointment at other times as necessary
Text: Bioinformatics & Functional Genomics, Pevsner, 2009, 2nd Edition
Week Date Day Chapter Readings and Topic
1 8/28 T Course overview; 1. Introduction; 2. Access to Sequence Data and Literature Information
1 8/30 R 2. Access to Sequence Data and Literature Information
2 9/4 T 3. Pairwise Sequence Alignment
2 9/6 R Computer Work
3 9/11 T Q, A – Computer Work
3 9/13 R 3. Pairwise Sequence Alignment
4 9/18 T A – Computer Work
4 9/20 R 4. Basic Local Alignment Search Tool (BLAST)
5 9/25 T Q, A – Computer Work
5 9/27 R 5. Advanced Database Searching
6 10/2 T A – Computer Work
6 10/4 R ***Lecture Exam 1***
7 10/9 T ** Monday Schedule** No Class
7 10/11 R 6. Multiple Sequence Alignment
8 10/16 T A – Computer Work
8 10/18 R 7. Molecular Phylogeny and Evolution
9 10/23 T Q, A– Computer Work
9 10/25 R 7. Molecular Phylogeny and Evolution
10 10/30 T A – Computer Work
10 11/1 R 10. Protein Analysis and Proteomics; 11. Protein Structure
11 11/6 T Q, A – Computer Work
11 11/8 R 8. Bioinformatic Approaches to Ribonucleic Acid (RNA); 9. Gene Expression: Microarray Data Analysis
12 11/13 T A – Computer Work
12 11/15 R ***Lecture Exam 2***
13 11/20 T 13. Completed Genomes
13 11/22 R Thanksgiving Holiday – No Class
14 11/27 T A – Computer Work
14 11/29 R **Annotation Project Due** 19. Human Genome
15 12/4 T Computer Work
15 12/6 R **Find-a-Gene Project Due** Wrap-up and review
12/12 W Cumulative Final Exam 2pm-3:50pm **Wednesday**
Q = Quiz, A = Assignment due Note: This schedule is subject to modification.
Course Grading: Your grade will be available at all times on the course website under the “Grades” tab. Please check your grade regularly in case of discrepancies and to gauge your progress in the course.
Lecture Exams (2 @ 100pts) 200
Cumulative Final 200
Assignments (10 @ 10pts) 100
Quizzes (4 @ 25 pts) 100
Annotation Project 100
Find-a-Gene Project 100