Cheryl Bailey University of Nebraska

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Syllabus
Fall, 2008
BIOC498: Bioinformatics

Faculty Instructor: Graduate Student Instructor: Teaching Assistant

Dr. Cheryl Bailey Stephanie Matejka Perry Ridge
Biochemistry Biochemistry Biochemistry
N106 Beadle Center N112 Beadle Center N108 Beadle Center
UNL 68588-0664 UNL 68588-0664 UNL 68588-0664
Phone: 472-3530
email: cbailey7@unl.edu email: steffie319@gmail.com email:perry.ridge@gmail.com


Office Hours: Contact Dr. Cheryl Bailey, Stephanie Matejka and Perry Ridge for an appointment.

Important note: The poster session is scheduled for dead week. Please let one of us know if that causes problems for you, or if you have any concerns about that.


Course Description: BIOC498 Bioinformatics is a 1 credit course in gene annotation.

Participation notice: This course is part of the Genomics Education Partnership (GEP), through Washington University in St. Louis, funded by the Howard Hughes Medical Institute. The Genomics Education Partnership is a collaborative opportunity to work as a research team through a large scale sequencing project. This is a dynamic student—scientist partnership to engage students in genomics research, which can conclude in publication of original research in genomics and science education. Assessment will include grades, online pre- and post-course surveys, university student surveys (CEIQ), oral presentations, poster session, and student feedback survey.


Course Objectives:

By the conclusion of the semester 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.


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/


Prerequisites:A biochemistry course.


Required Text: None.

Lecture Notes: The class notes will be posted under 'Lecture Notes' on the BIOC 431 Blackboard site. Many students find it useful to bring them to class and annotate them during the lectures. However, although a useful organizational tool, the lecture notes are not intended to be comprehensive and additional material will be presented in class.


Student Questions: If you have questions about the material in the course outside of class periods, weekly Discussion Board forums will provide communication between students, instructor, graduate student instructor and teaching assistant.

Teaching Methods: This class is project based, and will begin with lectures and active learning on the fundamentals of gene structure and annotation. It will quickly commence to student directed learning and collaboration on an assigned sequence that is approximately 20 kb.

Assignments:To provide you with practice and an opportunity to see how familiar you are with the material, there will be graded assignments, miniprojects, projectsand reaction opportunities.


Class Attendance: It is very important to attend class. Because this class is project based and collaborative, be there. Due to the distraction certain computer use can cause, only relevant web sites should be accessed during class time.

Course schedule:
Week 1 (Aug 25-29) Introduction to gene structure
Week 2 (Sept 2-5) Alternative splicing tutorial with help on blackboard
Week 3 (Sept 8-12) Introduction to evidence based gene finding
BLAST (Basic Local Assignment Search Tool) and NCBI
Week 4 (Sept 15-19) Miniproject 1: Annotation of 6.8
Week 5 (Sept 22-26) Miniproject 2: Annotation of 6.3
Week 6 (Sept 29-Oct 3) Miniproject 3: Annotation of 6.5
Week 7 (Oct 6-Oct 10) Team powerpoint presentations on annotation programs
Week 8 (Oct 13-Oct 17) Project: Fosmid sequence and project introduction
Week 9 (Oct 20-Oct 24) Fall Break
Weekly Blackboard progress report
Week 10 (Oct 27-Oct 31) Project: data analysis
Weekly Blackboard progress report
Week 11 (Nov 3 – Nov 7) Project: data analysis
Weekly Blackboard progress report
Week 12 (Nov 10- Nov14) Project data analysis
Weekly Blackboard progress report
Poster introduction
Chimp chunks
Week 13 (Nov 17-Nov 21) Project data analysis
Weekly Blackboard progress report
Project presentations
Poster update
Week 14 (Nov 24- Nov 28) Happy Thanksgiving
Week 15 (Dec 1- Dec 5) Construct gene model
Poster to printing service
Week 16 (Dec 8-Dec 12) Poster session. Last class
Note: This is during “dead week”. Let me know if you have
concerns about this timing.



Grading Policy:

Points that count toward your final grade.
Miniprojects 300 (100 x 3)
Team presentation 200 (200 x 1)
Weekly progress reports 100 (5 x 20)
Project presentation 200 (200 x 1)
Poster and poster presentation 200 (poster 100 + session 100)
Total 1000

The final grade will be determined by the number of points accumulated. The following grading scale will be used.
Grading Scale:
Final Grade From To
A+ 95% 100%
A 87% 94%
A- 84% 86%
B+ 80% 83%
B 75% 79%
B- 72% 74%
C+ 68% 71%
C 62% 67%
C-/No Pass 60% 61%
D+/No Pass 56% 59%
D/No Pass 50% 55%
F/No Pass 0% 49%
Grades will not be curved. If every member in the class knows 90% of the material, all should receive "A"s, and conversely, if no one is willing to expend the effort necessary to learn 90% of the material, there will be no "A"s.


Students with Disabilities:

Students with disabilities are encouraged to contact the instructor for a confidential discussion of their individual needs for academic accommodation. It is the policy of the University of Nebraska-Lincoln to provide flexible and individualized accommodation to students with documented disabilities that may affect their ability to fully participate in course activities or to meet course requirements. To receive accommodation services, students must be registered with the Services for Students with Disabilities (SSD) office, 132 Canfield Administration, 472-3787 voice or TTY.


Academic Dishonesty:

UNL's policies concerning academic dishonesty and grade appeals will be followed.


Created by CB & SM (ed. CB 8.25.2008)