Jennifer Myka - Galen College of Nursing

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Genomics at Galen College of Nursing

Dr. Jennifer Myka is currently working with collaborators to host undergraduates from neighboring institutions to include them in genome annotation projects as a part of GEP.  These students will be participating in genome annotation as part of their undergraduate research experience at their home institutions.

Genomics at TMC

While at Thomas More College, Dr. Jennifer Myka taught a 1 credit course, Biology 400: Genome Annotation, approved as an Independent Study and Research pilot course.  There were 4 students who worked together throughout the semester, including one TA, Tom Boeshart, who was trained during January 2007 at Wash. U.

Comments on Implementation at TMC

Course Structure:

Time:

For this pilot course, the TMC Biology Department approved 1 credit hour, which meant that students were expected to meet for only one hour per week.  However, these 4 students were quite motivated, and often stayed for 3-4 hours for each session, beyond the expectations required for the syllabus.

Projects versus Exercises: 

Because the four students who signed up for this course had not all completed the sophomore year Genetics course, much of the time had to be utilized to go over basic concepts required to understand the concept of genome annotation before students could begin working on projects. 

Resources:

The TMC Biology Department allowed the students to use 4 laptop computers during the scheduled weekly meeting times.  Dr. Myka "burned" CD's for the students containing all of the contig information and other GEP resources.  Students did not have access to sufficient computing power between scheduled sessions, so all work had to be done during the one scheduled hour per week plus any time the students could stay beyond the scheduled course time.

Other Comments:

Outcomes:

Very late in the semester, after working on some of the exercises from the GEP Wiki, students began work on a specific contig.  Before the semester ended, students had identified one gene and had worked through most of the four exons, delineating intron/exon boundaries, etc.  However, given the time made available in their schedules, and the large amount of background that needed to be covered before students were ready to work on actual genome annotation, the course was a success.

Syllabus for Bio400: Genome Annotation at TMC

Course: BIO400 Genome Annotation (Independent Study and Research)
Credit Hours: 1 credit hour
Semester: Spring 2007
Faculty Supervisor: Dr. Jennifer Leigh Myka
Course Description: Students can earn one to four credit hours in an independent study supervised by a departmental faculty member. These courses are recommended for juniors and seniors. (refer to TMC course catalog)


1. Nature of the Study:
This project will involve work in the following area:
   a. Genome annotation. This work would involve students working to:
        i. understand the process of genome annotation,
        ii. learn to find genes in DNA sequences, including start and stop codons, splice sites, and other gene features,
        iii. learn to use GenBank, On-line Mendelian Inheritance in Man, Pub-Med, and other sources of genomic information,
        iv. utilize resources available for genome annotation through Washington University’s Genomics Partnership,
        v. and collaborate with classmates to prepare a lab activity for future courses in genetics/molecular genetics.


2. Goals & Learning Objectives:
At the completion of this project, the student will be able to:
• explain to peers the process of genome annotation,
• be able to perform genome annotation on DNA sequences provided, and
• prepare the results of their collaboration as a lab activity for future TMC genetics/molecular genetics courses.


3. Evidence of Accomplishment:
Students will meet weekly with the faculty supervisor and participate in discussion of background research and results obtained through student work. Students will participate in a pre- and post-evaluation offered through Washington University in St. Louis. Students will prepare a lab activity for future TMC genetics/molecular genetics courses, and be able to explain this activity to both students and faculty.


4. Criteria for Evaluation, Grading, and their Application:

Students will be evaluated for their success in accomplishing the following project components: Students will regularly participate in discussion and practice sessions, and will coordinate with their peers to work together and individually as needed to complete the creation of a lab activity for future TMC genetics/molecular genetics courses. Students will diligently work towards project completion. Students will present their results to the broader TMC community by providing these materials to Biology faculty for use in future courses.


Grades will be assigned according to the following system:
• An “A” is considered “Superior Performance.” To achieve an “A”, students participate to their highest level of achievement, offer accurate insights into the project, read background material in a timely manner and integrate what they have read into the project, ask appropriate questions, and show progress towards creating the lab activity in a timely manner.
• A “B” is considered “Above Average Performance.” To achieve a “B”, students participate to a high level of achievement; often offer insights into the project, usually read background material in a timely manner, often integrate what they have read into the project, often ask appropriate questions, and generally show progress towards creating the lab activity in a timely manner.
• A “C” is considered “Average Performance.” To achieve a “C”, students participate to an average level of achievement; sometimes offer insights into the project, sometimes read background material in a timely manner, sometimes integrate what they have read into the project, sometimes ask appropriate questions, and show some progress towards creating the lab activity in a timely manner.
• A “D” is considered “Passing, but Below Average Performance.” To achieve a “D”, students participate to a passing but below average level of achievement; rarely offer insights into research analysis, rarely read background material in a timely manner, rarely integrate what they have read into the project, rarely ask appropriate questions, and show little progress towards creating the lab activity in a timely manner.
• An “F” is considered “Failure.” To achieve an “F”, student performance is absolutely unsatisfactory.


5. Arrangements for Consultation with Faculty Supervisor:

Students will meet with the faculty supervisor for at least one hour per week, on average, for discussion of background, project progress, and other issues including planning for upcoming laboratory work and for the final paper and presentation. Meetings will take place in S309 in Dr. Myka’s office, in S302 in the Biology Seminar, or in S310 in the Genetics Laboratory.


6. Preliminary Reading List:
Students will refer to the materials provided by Washington University’s Genomics Partnership, which includes extensive materials available via the internet, as well as references to general and primary literature sources.