GMS6231 - Genomics and Bioinformatics

(3 credits)

COURSE DESCRIPTION: Principles of genomic characterization and bioinformatic analysis of eukaryotes, including an overview of analytical platforms, computational tools, experimental design, analysis methods and databases used to study DNA sequence, gene expression and protein levels.
COURSE OBJECTIVES: Understanding the principles of genomic analysis of eukaryotes at various levels (DNA, mRNA and protein), and bioinformatics methods used in these analysis.
MEETING PERIODS: Tuesday (11:45am-1:40pm) & Thursday (11:45am-12:35pm).
WHERE: UFGI 451A (4th floor of UF Genetics and Cancer Research Complex, between the Cancer and Genetics wings).
OFFICE HOURS: By appointment.
COURSE WEBSITE: http://genome.ufl.edu/courses/GMS6231/
COURSE PREREQUISITES: STA6166 (Statistical Methods in Research I) and PCB5065 (Advanced Genetics), or permission from the instructor.
COURSE SYLLABUS: View complete course syllabus.
REFERENCES: Books:

A Primer of Genome Sciences (3rd edition, 2009), by Greg Gibson and Spencer V. Muse, Sinauer Associates, ISBN: 0878932321 (not required). Please note that this book can be purchased online as an eTextbook.

Required reading will be indicated by the instructor throughout the semester.
LECTURE SLIDES:
(password required)
Week 1 - DNA sequencing and alignment
Week 1 - DNA alignment - continued
Week 2 - DNA Alignment
Class notes - January 22 2013
Week 3 - Genome annotation and gene discovery
Class notes - February 5 2013
Class notes - February 7 2013
Outline for transcriptomics section
Introduction
review of hypothesis testing
Experimental Design
quality control
Detection
Normalization
differential expression
Proteomics-Lecture1note
Proteomics-Lecture2note
Proteomics-Lecture3note
Proteomics-Lecture4note
Proteomics-Lecture5note

PAPERS:
(password required)
  1. Carneiro et al., 2012
  2. Lam et al., 2012
  3. Loman et al., 2012
  4. Quail et al., 2012
  5. Clark et al, 2011
  6. Chatterjee et al, 2012
  7. Langmead et al, 2009
  8. Langmead et al, 2012
  9. Paper discussion 3 - First paper Paper discussion for January 31
  10. Paper discussion 3 - Second paper Paper discussion for January 31
  11. Paper discussion 3 - Third paper Paper discussion for January 31
  12. Paper discussion 1A
  13. Paper discussion 1B
  14. Paper discussion 2
  15. Paper discussion 3
  16. List of references
  17. April 5 paper discussion Please send me pros and cons of this paper before class
PROGRAMS AND DATASETS:
(password required)
The students need to complete a user agreement prior to be given access to the Fisher cluster. Access to the cluster is required for the course because several exercises will be done in that environment. User agreements need to be turned in to the instructor during the first week of class. To become familiar with Fisher and the rules for its usage, please see this page. Please note that fisher can only be accessed from inside the UF campus network. In order to access fisher from outside, please use the VPN client provided by UF IT services.


Students are also required to install JMP Genomics on their personal computers. Please contact Joseph Kelly for information on how to obtain and install the software.
  1. Please download and install the following programs:
    PuTTY (Windows)
    WinSCP (Windows)
    CyberDuck (Mac)
  2. Introduction to the Unix command-line
  3. A Unix reference card.
  4. SAM format specification
  5. SNP calling with SAMtools
PROBLEM ASSIGNMENTS:
AssignmentDue date
experimental design file
design_no54
INSTRUCTORS:
Dr. Sixue Chen
Department of Biology
College of Liberal Arts and Sciences
Cancer & Genetics Research Complex, Rm. 438
Phone: (352) 392 3277
e-mail: schen@ufl.edu

Dr. Lauren McIntyre
Department of Molecular Genetics and Microbiology
College of Medicine
Cancer & Genetics Research Complex, Rm. 116
Phone: (352) 273 8024
e-mail: mcintyre@ufl.edu

Dr. Matias Kirst (Course leader)
School of Forest Resources and Conservation
College of Agriculture and Life Sciences
Cancer & Genetics Research Complex, Rm. 320
Phone: (352) 846 0900
e-mail: mkirst@ufl.edu

GRADES: 40% Exams (3 exams on DNA sequencing, transcriptomics, and proteomics, equal weight)
40% Projects (4 projects, equal weight)
10% Article discussions
10% Class participation
ACADEMIC HONESTY: As a result of completing the registration form at the University of Florida, every student has signed the following statement: "I understand that the University of Florida expects its students to be honest in all of their academic work. I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University".
ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES: Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodations.
UF COUNSELING SERVICES: Resources are available on campus for students having personal problems or lacking clear career and academic goals, which interfere with their academic performance. These resources include:
  1. University Counseling Center, 301 Peabody Hall, 2-1575, personal and career counseling;
  2. Student Mental Health, Student Health Care Center, 2-1171, personal counseling;
  3. Sexual Assault Recovery Services (SARS), Student Health Care Center, 2-1161, sexual assault counseling;
  4. Career Resource Center, Reitz Union, 2-1601, career development assistance and counseling.
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