Experimental Biology Lab: Comparative Genomics
The computer analysis of genetic information is increasingly vital for biological research and in applications ranging from drug development to nature conservation. This course aims to provide first-hand experience in this area. It begins with lectures introducing the genomics databases, the molecular biology behind the data, and the computational techniques used to analyze it. Concurrently, computer labs provide hands-on learning on searching the databases, analyzing the data, and using scientific literature. Each student finishes the semester by independently designing and executing an original research project, after which they submit a written paper and give a talk presenting their results.
What is Comparative Genomics?
What type of genomics databases are available?
And how are they accessed?
What is the molecular biology behind the analyses?
What types of analyses are available?
The course consists of two parts: (1) an introductory part, during which we will introduce you to some tools that are used in comparative genomics and discuss the scientific method in general; and (2) a project part, during which you design, perform, and present a small comparative genomics research project.
During the introductory part, you will have home assignments every week (8 in total). The assignments are due the following week and give 2 points each (total 16 points). During the project part you will first write a two-page project proposal before starting on your research. When you have completed your study, you write a 10-page scientific report. Finally, you present your project orally in front of the rest of the students. The project proposal can give you 14 points total, the project report 50 points, and the oral presentation 20 points, for a total maximum for the course of 100 points. These points are translated to grades as follows: 100-90 (A), 89-80 (B), 79-70 (C), 69-60 (D), 59-0 (F).
It is essential that each proposal, report, and oral presentation contains a significant amount of original material. Copying material from other students or from the web without giving due credit to the original source will automatically result in an F grade for the course, in addition to other disciplinary actions that might be taken by FSU.
See under 'Assignments' (link on the left side of this page) for more information on the grading expectations.
We highly recommend the following texts, but do not require you to buy them.
1A. Lecture: Introduction (Fredrik Ronquist)
1B. Lab: Introduction to Linux
2A. Lecture: Library Resources at FSU (Presented by Michael Luesebrink)
2B. Lab: Literature Searching
3A. Lecture: Genomics Web Resources (Steve Thompson)
3B. Lab: Genomics Databases and Tools
4A. Lecture: Similarity Searching and Pairwise Alignment (Steve Thompson)
5A. Lecture: Multiple Sequence Alignment (Steve Thompson)
5B. Lab: Multiple Sequence Alignment
6A. Lecture: Phylogenetics I (Fred Ronquist)
6B. Lab: NJ and Parsimony
7A. Lecture: Phylogenetics II (Fred Ronquist)
7B. Lab: Phylogenetics II
8A. Lecture: Phylogenetics III (Fred Ronquist)
8B. Lab: Phylogenetics III
9A. Lecture: Scientific Writing
9B. Lab: Writing a Project Proposal
10. Mandatory Project Counseling
11. Mandatory Project Counseling
12-14. Work on Individual Project
14. Written Report Due
15. Oral Presentation
Attendance is compulsory the first day of the course (FSU policy). Attendance is also compulsory for the individual counseling session (on March 22) and the oral presentations the last day of the course (April 19). Attendance during the lectures and lab sessions is highly recommended but not mandatory. Lectures and lab tutorials will be made available on the course web site (on the FSU Blackboard system).
Florida State University provides high-quality services to students with disabilities, and we encourage you to take advantage of them. Students with disabilities needing academic accommodations should:
(a) register with, and
provide documentation to, the Student
Disability Resource Center (SDRC) in room 108 in the Student Services
Building (644-9566); and
Academic Honor code
Students are expected to uphold the Academic Honor Code published in The Florida State University Bulletin and in the Student Handbook. The first paragraph says: The Academic Honor System of Florida State University is based on the premise that each student has the responsibility to uphold the highest standards of academic integrity in the student's own work.
© 2013 Steven M. Thompson, acknowledgements and thanks to the Florida State University Biology Department for generously extending Web hosting and e-mail services beyond my FSU tenure. firstname.lastname@example.org