Laura Reed

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Integrated Genomics at University of Alabama Tuscaloosa

Course Overview

This advanced undergraduate/graduate level course introduces the major technologies and concepts in genomics, familiarizes students with some publicly available of bioinformatics databases and tools, contributes to the public knowledge base through student-lead bioinformatics and literature based research, and gives students hands-on experience with genomics wet lab methods. This course will also provide information on careers in biotechnology.
The course is based on a mixture of lectures, labs, in-class problem sets, and discussions of the current literature. The course also includes presentations of student research projects and wikipedia page update. The course is organized around Drosophila as an excessible genetic and genomic tool.

Implementation

The first time this course was offered in Fall 2011 it was designed to provide both wet lab and bioformatics research experience training for advanced undergraduates.  I used the GEP for a portion of bioinformatics component, requiring the students to complete the annotation of one "difficult" D. mojavensis fosmid.  In addition to this assignment, the students were performing wet lab proceedures (e.g. DNA extraction, q-RT-pcr) and updating one genomics-related stub entry on wikipedia.  I taught the course in a similar manner in Fall 2012 and will again in Fall 2013.

Lessons Learned and Future Plans

In the future, I plan to have the students first annotate a relatively "easy" fosmid and then follow-up with a difficult fosmid as approiate (honors, extra credit, graduate students?).  Despite the preliminary exercises some of the students were overwhelmed by working on a difficult fomsid and a more stepwise introduction would have been helpful to them.  I also plan to use a modified version of the preliminary exercises in Fall 2013.  In general, I found GEP to be an excellent compliment to the other activies in the course to introduce students to the diversity of activities that happen within genomics research. 



Syllabus BSC 442 Section 001: Integrated Genomics
Fall 2012
4 Credit Hours
Primary Instructor: Dr. Laura Reed
Prerequisites

From the Student Records System
BSC 300 (undergrad)
And
BSC 315 (undergrad) (may be taken concurrently)
Course Description

This advanced undergraduate level course will introduce you the major technologies and concepts in genomics, familiarize you with some publicly available of bioinformatics databases and tools, contribute to the public knowledge base through your own bioinformatics and literature based research, and give you hands-on experience with genomics wet lab methods. This course will also provide information on careers in biotechnology.

The course will be based on a mixture of lectures, labs, and in-class problem sets. The course will also include presentations of your research projects and wikipedia page update.

Assignments will be provided, returned, and graded electronically whenever possible. The course will be administered through Blackboard.

Enthusiastic participation in lectures and discussions, as well as in your research project, is critical to your ultimate good performance in this course.

You will also be expected to come prepared for the day's lab assignment having done any assigned reading or pre-lab work. Pop quizes will be used to enforced these prepartion measures if necessary.

Excessive use of electronic devices during class (e.g. texting, web surfing) will result in dismissal from the class session and loss of participation points for that session.

Proper lab attire (closed-toed shoes and long pants) must be worn at all times. Failure to come dressed appropriately will result in dismissing from class, loss of participation points and any opportunity to complete the assignment for that session. This is for your own safety.

Absolutely NO food or drink allowed in the classroom/laboratory. You will be immediately dismissed with a loss of participation points and any opportunity to complete the assignment for that session. This is for your own safety.

In addition to the required text, students will be required to have their own bound lab notebook and 1GB USB thumb drive.


Student Learning Outcomes

At the conclusion of this course students will be able to:

Describe the basic methodologies of the major technologies in genomics and systems biology.

Demonstrate understanding of the general concepts underlying genome sequencing and annotation.

Demostrate understanding of the technologies and methods for performing basic nucleic acid lab techniques.

Write a properly-cited literature based Wikipedia entry on a specific genomics topic.

Demonstrate improved oral presentation skills.

Outline of Topics

Databases, Sequencing Technologies, Human Genome Project, Genome Annotation, Population Genetics/Molecular Evolution, Genetic Mapping, Gene and Genome Duplications, Networks, Chip Technologies, Gene expression analysis, Next Generation Sequencing, Personalized medicine, Systems Biology, DNA and RNA isolation, PCR and primer design, Quantative PCR

Exams and Assignments

See class schedule for more details.

Individual Assignments:

Lab Exercises

Wikipedia Page Entry and Presentation

Mid-term and Final Exam

Annotation Project/Presentation

Group Assignment:

Drosophila Mutatant Analysis Project/Presentation


Grading Policy

Undergraduate Grading Criteria:

Wikipedia Page Update and Presentation 20%

Fly Wetlab Project and Presentation 20%

Annotation Project and Presentation 20%

Midterm Exam and Lab Notebook Evaluation 10%

Final Exam and Lab Notebook Evaluation 10%

Participation 10%

In class worksheets/problem sets 10%


The MINIMUM percentage points required for each final letter grade are as follows:

97.0% = A+ 87.0% = B+ 77.0% = C+ 67.0% = D+ 0% = F

93.0% = A 83.0% = B 73.0% = C 63.0% = D

90.0% = A- 80.0% = B- 70.0% = C- 60.0% = D-


Graduate Grading Criteria:

Wikipedia Page Update and Presentation 15%

Fly Wetlab Project Write-up 15%

Annotation Project and Presentation 15%

30 Minute Genomics Lecture 15%

Written proposal for genomics research 15%

Midterm Exam and Lab Notebook Evaluation 5%

Final Exam and Lab Notebook Evaluation 5%

Participation 10%

In class worksheets/problem sets 5%

The MINIMUM percentage points required for each final letter grade are as follows:

90.0% = A 80.0% = B 70.0% = C 60.0% = D

The instructor reserves the right to lower the requirements for each grade but not raise them. Each student's final percentages for each grading category will be normalized to the top student score in that category.


Policy on Missed Exams & Coursework

If you miss a scheduled presentation date you will be required to schedule a make-up presentation with Dr. Reed and an additional assignment may be given.

Late assignments will only be accepted for one week following the due date and will be worth only a maximum of 50% of their original credit. Assignments turned in within 24 hours of the deadline will receive a maximum of 90% of the original credit.

Attendance Policy

Attendance is mandatory. Missing class without a medical or pre-approved excuse will result in the loss of one full letter grade from the class participation component of your grade.
Required Texts

UA Supply Store Textbook Information
Textbook data from the Supply Store not found for this course.

Other Course Materials

Bound laboratory notebook (more details given the first class).

1GB USB thumb drive.

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