Todd Eckdahl - Missouri Western State University

From GEP Wiki
Jump to: navigation, search

Genomics at Missouri Western State University

At MWSU, Dr. Todd Eckdahl of Biology and Dr. Jeff Poet of Mathematics teamed up in the spring semesters of 2007, 2009, and 2011 to teach a 2 credit course, Biology 331: Bioinformatics.  In 2007 and 2009, the course was entirely devoted to using GEP materials to engage the students in annotation of Drosophila genes. In 2011, the course was divided into two sections.  During the first half of the semester, students worked on Drosophila annotation and during the second half they worked on bioinformatics projects of their own choosing.

Comments

Time: Beginning in 2009, and continuing in 2011, the couse was scheduled with a three hour block of time per week.

Projects versus Exercises: In 2007, we spent the first four weeks of our 14 week semester working on exercises. Although the students (and faculty) learned from this, we moved more directly into the annotation projects in 2009 and learned along the way. We continued this approach in 2011.

Outcomes: The students learned a lot from the experience of doing something that they had not done before. They made more progress on projects as time was running out. In 2007, some of the projects were completed and submitted, but all of them were submitted in 2009 and 2011. In each of the years, all the students prepared oral presentations for the class and poster presentations for a campus poster day.

Syllabus for Biology 331 - Bioinformatics

Biology 331 - Bioinformatics Syllabus
Spring 2011

Missouri Western State University

Dr. Todd Eckdahl, SM201, Biology, eckdahl@missouriwestern.edu
Dr. Jeff Poet, SM113H, Computer Science/Math/Physics, poet@missouriwestern.edu

Class meets Tuesdays 8:00-10:50 in the Agenstein 323 Computer Lab. Attendance to the weekly class meeting is MANDATORY.  Two or more unexcused absences will result in an F for the course.    

Objectives – This course is designed to enable students to participate in a nationally distributed DNA sequence annotation research project.  Students will learn to use online tools and to sequence analysis software to annotate original DNA sequences.  Students will work in pairs to complete independent projects that explore original biological questions.  Results will be presented orally to the class and in poster form at the MWSU Multidisciplinary Research Day.
 
Grading - Grades will be determined by the following.

A. Class assignments and homework worth 20% of grade.

B. Conducting Distributed Genome Annotation Project
1) Gene annotation report (individual) 10%
2) Oral presentation of annotated gene (pairs) 10%
3) Poster presentation of fosmid (group) 10%
4) Contribution of data to Genomics Education Partnership 10%

C.   Conducting independent Bioinformatics research project as pairs
1) Project proposal 10%
2) Contribution to class Wiggio page of Bioinformatics resources 10%
2) Oral presentation to class 10%
3) Poster presentation at Multidisciplinary Research Day 10%

Grading Scale - 90% - 100% = A, 80% - 90% = B, 70% - 80% = C, 60% - 70% = D, < 60% = F

Course Schedule

• Over the first couple weeks of the semester, the class will work together to explore several of the most used databases and software tools.  During this time, students will learn how to analyze genomic data (including annotation of genes, assessment of repeats, exploration of evolutionary questions, etc.). 
• Early in the semester the class will claim 3-4 fosmids of DNA sequence data from Drosophila
• Each student will be assigned a gene to annotate, contributing to a distributed research project
• Work on annotation will continue for the first half of the semester
• For the second half of the semester, students will develop proposals and conduct independent bioinformatics research projects as pairs 

Note: Any student in this course who has a disability that prevents the fullest expression of his or her abilities should contact us as soon as possible so that we can discuss class requirements.