Experimental Biology Lab: Comparative Genomics

Course Statement

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.

The Syllabus is here, and a stripped down Course outline is here.

Instructors

Fredrik Ronquist and Steve Thompson of FSU's School of Computational Science and FSU's Biology Department; and Teaching Assistant Clemens Lakner of FSU's Biology Department

What is Comparative Genomics?

• The DOE's perspective
• and a nice PLOS Biology article.
• to compare . . . within and across species . . .
• genomes: the complete genetic (DNA) complement of an organism.

What type of genomics databases are available?

• sequence -- protein (e.g. SwissProt) and/or DNA (e.g. GenBank)
• mapping -- linkage associations (where is the sequence in the genome?)
• literature -- e.g. PubMed references

And how are they accessed?

• often through a browser, e.g:
• NCBI Genomes
• Online Mendelian Inheritance in Man
• Human Genome Database
• Stanford Genomic Resource
• Indiana University's FlyBase
• The Institute for Genomic Research (TIGR)
• but dedicated software too
• the Accelrys GCG Wisconsin Package

What is the molecular biology behind the analyses?

• the Central Dogma: DNA --> RNA --> protein
• complications: alternative splicing, RNA editing, prions, etc.
• Homology: relationship by descent!

What types of analyses are available?

• You can search for related sequences using dedicated software, such as
• The Accelrys GCG Wisconsin Package
• or using World Wide Web services, such as
• Blast at NCBI
• FastA at the University of Virginia
• You can align and analyze sequences using small programs like
• ClustalW
• or larger packages like GCG or Web services such as
• TIGR software
• PipMaker and MultiPipMaker
• Comparative Genomics Center at Lawrence Livermore National Laboratory
• Southwest Biotechnology and Informatics Center
• Comparative studies usually require the inference of evolutionary trees (phylogenies) using commercial software or freeware such as
• PHYLIP
• PAUP
• MrBayes
• Therefore, comparative genomics (or part of it) is sometimes referred to as phylogenomics

Grading

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.

Office Hours:

Fredrik will be available in his office (Dirac Science Library 150-U) Tuesdays from 3:00 pm - 5:00 pm during course days. During the individual project period, at least one of the instructors or the teaching assistant will be available on Tuesdays from 11 am to 3 pm in the classroom (Dirac 152).

Suggested Texts:

We highly recommend the following texts, but do not require you to buy them.

• Phylogenetic Trees Made Easy by Barry G. Hall; Sinauer Associates, Inc. Second edition.
• Writing Papers in the Biological Sciences by Victoria E. McMillan; Bedford/St. Martin's. Third edition.

Computer and Classroom Access

At the beginning of the course, you will be given a SCS student account that will allow you to log onto the course computers and the Mendel server, which runs the GCG package and hosts local copies of the most popular genomics databases. The user account will allow you to use these resources from anywhere at any time using SSH client software and an X Windows client (see under 'Links' in the left menu) . If you prefer working in the classroom, the workstations there are available for you on a first come first serve basis during weekdays, 8 am to 5 pm, when no other activities are scheduled (see calendar here). At the beginning of the course, we will be collecting information about your FSU Card. After about a week, you should be able to use your FSU Card to gain access to the classroom. Simply swipe your FSU card to open the classroom door. Unfortunately, we are not able to arrange after-hours access to the computers.

Requesting an Account

If you added the course late, you may have to apply for a user account on your own. To do this, fill out the form here. Be sure to specify that you are a student in the Comparative Genomics class (course number BSC 3402L, section 5).

Attendance

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).

ADA Statement

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

(b) bring me a letter from SDRC indicating your needed academic accommodations. Please do this during the first week of class.

For more information on this see the Resource Center's web site.

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.