Kelly Reed - Austin College
Bioinformatics was offered as a topics course in biology in Fall 2007. This was the first time the course was offered at our institution. Since we are a small liberal arts college, it wasn’t too surprising that I ended up with only four students enrolled in the course. Interestingly, two of the students were biology majors, one was a math major and one was a computer science major. I used Genomics, Proteomics, and Bioinformatics by Campbell and Heyer as the text for the course. The course met twice a week for 80 min and once a week for 3 hours. The 80 min sessions were spent discussing case studies presented in the Campbell/Heyer book and the 3 hour session was primarily spent on annotation ofD. erecta fosmids. Nine lab sessions were devoted specifically to the annotation project and as such each student was responsible for annotation of a different fosmid. Because the class size was small and a significant amount of time was set aside for the project, I choose four overlapping fosmids (all level 3 difficulty) for the students to annotate.
The second time I taught the course in Fall 2008, the course was renamed Genomics to better reflect what was taught in the course. This time, in addition to annotation of Drosophila, students also annotated genes from a bacterium for particular biochemical pathways. The remainder of the course was pretty much the same as the first time through.
IMPLEMENTATION OF ANNOTATION PROJECT:
Fall 2007: None of the students in the course had previous experience with BLAST or CLUSTAL so the first three lab sessions were spent introducing them to NCBI BLAST and CLUSTAL analyses via Biology Workbench. The students then worked through a few of the GEP tutorials and exercises including A simple introduction to NCBI BLAST and Detecting and Interpreting Genetic Homology. In addition, they developed and tested hypotheses using the ALIVE Study data available in the HIV Problem Space on the BioQuest BEDROCK website (a link was available from the GEP curriculum page). These activities allowed the students to become more confident in accessing and analyzing genomic data. I then walked the students through the Annotation for D. virilis PowerPoint presentation to illustrate the general strategies they might use to annotate their fosmid. During the remainder of the course (9 lab sessions), the students worked on their own annotation project. I also had a senior biology major who had gone through the TA training to serve as a teaching assistant for the annotation project.
Fall 2008: I basically implemented the project in the same way as 2007. However, I spent less time on Drosophila annotation this year so that students would have time for bacterial annotation as well.
LESSONS LEARNED AND FUTURE PLANS:
Fall 2007: Overall, the project went well. The first few weeks, the students were a little unsure of themselves and needed quite a bit of guidance but as they got into the project they seemed to gain independence. I encouraged them to work through the straightforward gene models first and then tackle the more difficult ones. I never told the students that they had overlapping fosmids and it took them about 2/3 of the semester until they figured it out on their own. So near the end of the semester, they were able to compare the overlapping gene models and this turned out to be a good exercise in itself. While the students presented their work both orally and in a written report at the end of the course, I never required them to submit any updates during the course of the semester. I am planning on teaching the course again in Fall 2008 and currently I have 5 students enrolled. I have also recruited one of the Fall 2007 students to serve as a TA for next year’s course. One thing I will do differently is that I will have students present annotation updates every few weeks throughout the semester. I think this will be particularly important with a larger class size.
Fall 2008: Actually, I think the students learned a great deal about the differences in gene organization between eukaryotes and bacteria by annotating genes from both types of organisms. For the Drosophila annotation, I did have students give bi-weekly updates of where they were in the annotation process. This was helpful to keep them moving forward at an adequate pace and also to see any problems they had encountered. I have found it invaluable to have a student teaching assistant to help answer questions especially at the beginning of the project.
SYLLABUS FOR BIOLOGY 350 BIOINFORMATICS - FALL 2007
Dr. Kelly Reed– Moody Science 306 Phone: 903-813-2064 Office Hours: M 2-4 pm, TH 1-3 pm, or by appointment
COURSE MEETING TIMES AND CLASS ATTENDANCE:
TTh 9:30 – 10:50 am, Lab – W 1:30 – 4:20 pm
The TTh morning course meeting will take place in Moody Science 112A and the Wednesday lab session will meet in the Keck Computer Lab. You are expected to attend all class meetings unless there is a valid excuse in which case you should contact me prior to class and let me know. If you are ill, you should email me or leave me a phone message prior to class. If you will miss class due to an approved college activity, you need to make arrangements with me ahead of time. If you have an unexcused absence from class, you will receive a zero on that day’s assignment.
Campbell, A.M. and Heyer, L.J. 2007. Discovering Genomics, Proteomics, and Bioinformatics. Pearson Education Inc., San Francisco, CA. There is a companion website to go along with the book that you will find extremely helpful. http://wps.aw.com/bc_campbell_genomics_2/0,11571,2875502-,00.html
This textbook is very different than most other science texts. The entire text is developed from biological case studies from the scientific literature. Discovery Questions are imbedded throughout the text to challenge you to think about the information being presented to you in more depth and gain experience with extracting information from online genomic databases used by scientists.
- Become familiar with genomic methods and computer tools.
- Learn to think on genomic scale.
- Develop confidence and skills to analyze genomics experiments.
- Annotate a 40 kb segment of the Drosophila erecta genome.
- Appreciate how math and computer science can be used to better understand biology.
Tuesday/Thursday Classes: The Tuesday/Thursday morning classes will be devoted to working our way through portions of Discovering Genomics, Proteomics, and Bioinformatics as indicated in the course schedule. The format of each class will require all of you to read each day’s assignment BEFORE you come to class. During each class, we will discuss the days reading and go over the assigned Discovery Questions. I will also present some concepts in the traditional lecture format. I will assign some Discovery Questions to be answered in writing and submitted to turnitin.com by 9 am the following day of class. In order to fully understand the material, you will need to use the web links and answer the Discovery Questions. Forty percent of you grade in this course will depend on your participation in this process (reading the material, answering the discovery questions, and participating in class discussions). There will not be any exams in the course.
The first three lab sessions will be spent introducing you to some of the tools and techniques necessary for genome annotation. The remainder of the lab sessions will be devoted to a research project with other undergraduates around the country aimed at addressing whether or not heterochromatic and euchromatic domains of a genome can be distinguished based on sequence organization and/or characteristics of the genes in these different environments. This project comes from the research of Dr. Sarah Elgin from Washington University in St. Louis. Several years ago, she developed a consortium so that undergraduate researchers could participate in a genomics level research project. Thus far, this research has resulted in one group publication (Genome Biology 2006 7:R15) with additional publications anticipated in the future. For a complete description of this lab project, see the attached handout. In order for you to be considered for publication based on your work on this project, you must successfully annotate your own 40 kb fosmid of D. erecta. This success is determined by how well you document your annotation by providing appropriate genomic evidence. You will submit a written report and also present your findings via an oral PowerPoint presentation.
Participation in class and preparation before class is vital. We will frequently be discussing a variety of topics including the design of experiments, evaluation of presentations and progress on your project. You should come to class properly prepared and ready to contribute. Course grades will be determined as indicated below.
- Discovery Questions - 25%
- Class Participation - 15%
- BLAST tutorial (DQ2.3,2.4) - 4%
- BLAST exercise: Detecting and Interpreting Genetic Homology - 8%
- Exploring HIV Evolution - 8
- D. erecta fosmid annotation
- written report - 30%
- oral presentation - 10%
In general, final grades will be determined as follows: 90-100%, A; 80-90%, B; 70-80%, C; 60--70%, D; 0-60%, F. Plus and minus grades will be awarded. To receive a grade of "S" for BIOL350 under the S/D/U system, you must achieve a 70% or higher. A course average between 60-69% will result in a “D” and a course average below 60% will result in a grade of "U".
STUDENTS WITH DISABILITIES:
Austin College seeks to provide reasonable accommodations for all individuals with disabilities and complies with all federal, state, and local laws, regulations, and guidelines. It is the responsibility of the student to register with and provide verification of academic accommodation needs to the Director of the Academic Skills Center (Laura Marquez, Wright Campus Center, Room 211) as soon as possible. The student also must contact the faculty member in a timely manner to arrange for reasonable academic accommodations. For further information call 903-813-2454 or visit the Academic Skills Center. College policy prohibits instructors from accommodating learning disabilities without first having received the proper written instructions from the Director of the Academic Skills Center.
You are expected to adhere to the Austin College guidelines concerning academic integrity. In other words, DO YOUR OWN WORK!!!! In addition, it is essential that you properly cite any references that you use. If you are unsure how to do this, please ask. Improperly citing references is a form of plagiarism.