Stephanie Mel Univ of California San Diego

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Genomics at University of California San Diego

Course Overview

Administrative:  The University of California, San Diego is a large public institution with over 20,000 undergraduates.  During the 2009 - 2010 Academic year, there were approximately 6000 Biology majors.  I accepted 20 Biology undergradates for the GEP course -- of the students who applied to take the class, only those who earned a B or higher in the prerequiste course (Molecular Biology lecture) were invited to enroll.  We met 2 times a week for 2 hours, for a total of 4 hours of class time/week.  Class took place in a Mac computer lab where each student had a computer to work on.  The course was co-taught by myself and an outstanding TA, Paul Bilinski. 

Update June 2012:  Due to budget cuts at the University of California, a stand-alone course was not taught during the last 2 years.  I am currently planning to adapt GEP materials so they can be used as a small module within a lab course, or as an exercise associated with a Molecular Biology lecture course.  Stay tuned!


General Course Structure:  We broke the material into 5 general sections:

1.  Introduction to BLAST

2.  DNA Sequencing

3.  Introduction to Finishing/Consed

4.  Annotation

5.  Claiming and Submitting Annotation Projects


Students were also evaluated with a homework (15%), 2 quizzes (15%) and (30%), an oral presentation (15%) and a final written report (25%). 

Implementation

Following are a few worksheets, homeworks, and quizzes used in the course

Course Evaluation

Positive:  We had tremendously positive feedback from students for the course.  Because all of the Biology classes at UCSD are so large, students loved having the opportunity to work closely with faculty on a research based problem.   The flow of information was good, starting with basic DNA sequence information and sequencing techniques and working through Consed and then annotation.   The exercises and homeworks were successful and the quizzes were a very good way of evaluating student learning. 


Needs Improvement:  Consed was the least favorite aspect of the course for many students, especially because we did not do actual finishing projects.  I would spend less time on this next time, or incorporate it differently.  Also, Paul and I did not feel as prepared as we would have liked to deal with difficult repeat DNA sequence issues, or with difficult annotation problems.  But this would obviously get better the next time around!  Getting our institutional IRB was a long, nightmarish process, so if your institutional board is picky, be sure to start the application process early! 


Sadly, University of California budget cuts have forced the elimination of this course for the time being, but we hope to have it back up and running at some point in the future. 

Syllabus for BIMM 173, Research Explorations in Genomics


Undergraduate Research Explorations in Genomics
BIMM 173 Spring 2010
Monday/Wednesday 10 AM – 12 PM
3070 York Hall

Instructors: Dr. Stephanie Mel and Paul Bilinski
4070E York Hall
858-822-0603
smel@ucsd.edu

pbilinsk@ucsd.edu

Office Hours: Dr. Mel: by appointment
Paul – Monday 12 – 1 PM, or by appointment

General Overview of Course: This course is a new addition to the Genomics Education Partnership program (http://gep.wustl.edu/). This innovative educational initiative is a collaboration between a number of colleges and universities around the country and the Biology Department and Genome Sequencing Center of Washington University in St. Louis. Participating undergraduates learn to take raw genome sequence data to high quality finished sequence, and to annotate genes and other features.

Course Objectives:
By the end of the quarter, you should have the skills to do the following:
Deduce gene function from sequence data.
Identify similar sequences and conserved domains in other organisms.
Identify promoter sequences and open reading frames.
Identify introns and exons
Identify imbedded repeats
Differentiate between protein coding sequences and pseudo genes.
Relate amino acid sequence, structure, and function
Evaluate relevance of available data
Construct a gene model
Discuss a specific gene within the context of the gene model
Articulate relationship of a gene to the biology of the organism.
Compare gene in evolutionary context to other homologs

Important databases:
To be successful in this course, you will navigate the following databases
(including but not limited to):
NCBI http://www.ncbi.nlm.nih.gov/
BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi
PubMed http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
Entrez http://www.ncbi.nlm.nih.gov/sites/gquery
FLybase http://flybase.bio.indiana.edu/
UCSC http://genome.ucsc.edu/
GEP http://www.gep.wustl.edu/

Grading:
Homework (15%)
Quiz #1 (15%), Quiz 2 (30%)
Oral Presentation (15%), Final Written Report (25%)