Comparative Genomics

Syllabus Fredrik Ronquist's Home Page Steve Thompson's Home Page GCG Workshops CSIT School Biology Department

Spring Semester 2005. Lectures - Tuesdays from 11:00 to 12:15 AM, in Dirac 152;
Laboratory - Tuesdays from 1:00 to 3:00 PM, also in Dirac 152. Credit hours: two

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 Course Syllabus is found here.

Your project, and what we expect from you for your grade.

Section	Max Points
Lab Assignments (8 @ 2 points)	16
Project Proposal	14
Research Paper	50
Oral Presentation	20
TOTAL	100

Points will be translated to grades as follows:
A: 90-100
B: 80-89
C: 70-79
D: 1-69

The following criteria should be met to obtain the full score for each item:

1. Lab Assignments (8 assignments worth 2 points each; in total 16 points):

• The assignment should be handed in on time (due at the following week's lab session) (1 point deducted if late)
• The assignment should be machine printed, legible and well organized
• The name of the student should be clearly indicated.
• The length should not exceed one page unless otherwise stated.
• The given assignment should be adequately addressed

2. Project Proposal (14 points; due on March 22 at 11 am):

• The proposal should be handed in on time in three identical copies (3 points deduction if late).
• The proposal should be machine printed (not hand-written), legible and well organized (all margins should be 1 inch; pages should be paginated). It should be stapled together.
• The proposal should not be more than two pages long (excluding References) and it should be printed using 12 pt serif font and single line spacing.
• The language should be such that a fellow student would be able to read the proposal and understand its content.
• The proposal should contain the following sections or items: Series Title, Title, Author, Background, Aim, Methods, and References.
• The Series Title should be given at the top of the first page (12 pt font, italics, centered) and should read: Project Proposals, Comparative Genomics, Fall -04.
• The Title of the proposal should be short and descriptive (bold 14 pt sans serif font, centered).
• The Author should be given (name, email address) (centered).
• The Background section should explain why the question being asked is of interest.
• The Aim section should clearly state the scientific question being asked. It should also derive testable predictions relevant to the proposed project.
• The Methods section should describe how these predictions are to be tested.
• The References section should list all the cited references in a consistent format. The references should be correctly and consistently cited in the proposal text.
• Each one of the headings Background, Aim, Methods, and References should be on a separate line (14 pt font, bold, left-aligned).

3. Project Report (50 points; due on April 14 at 5 pm):

• The report should be handed in on time in two identical copies (5 points deduction if late).
• The report should be formatted as a research article for the journal "Molecular Biology and Evolution". Detailed instructions on the preparation of the manuscript can be found here. It should be stapled together.
• The manuscript should be between 10 and 20 pages long (double line spacing, 12 pt font) (excluding figure legends, tables, and figures). The length should be appropriate considering the scope of the article.
• The language should be such that a fellow student will be able to read the report and understand its content.
• The Introduction section should clearly state the question in focus and why it is of general interest. It should also briefly describe how it was addressed in the project. The introduction should summarize background information from at least two major scientific papers that are directly relevant to the topic of the report.
• The Materials and Methods section should briefly describe the data and how it was obtained. It should also describe the methods used to analyze it.
• The Results section should give the main results of the analyses, preferably in the form of figures and tables (appended to the end of the report). The Discussion section should discuss how these results relate to the question being asked. It might well turn out that the results did not answer the question being addressed in the project, typically for reasons that were impossible or difficult to anticipate when the project was designed. This is OK and will not result in points being lost. However, the results still need to be summarized and there must be a discussion on why the results did not answer the question being asked and some suggestions for how the project could be modified to address the question. The Results and Discusssion sections can be combined.
• The Literature Cited section should list all the cited references in the format required by Molecular Biology and Evolution. The references should be cited in the main text of the report according to the Molecular Biology and Evolution format.
• The Table section should have each table, complete with short title, on a separate page.
• The Figure section should have each figure on a separate page with the corresponding figure legend at the bottom. Alternatively, all figure legends can be listed together on a separate page preceding the figures.
• Each one of the headings Introduction, Materials and Methods, Results, Discussion, and Literature Cited should be on a separate line (14 pt font, bold, left-aligned).

4. Oral Presentation (20 pt):

• The presentation should be 8 minutes long (4 points deducted if longer)
• It should be possible for fellow students to understand the presentation
• The presentation should state the question being asked and briefly describe the method used to address it
• The main result(s) should be presented in the form of one or a few simple diagram(s) or table(s) that are easy to understand.
• The figure(s) or table(s) should be presented either in a hand-out or (preferably) as powerpoint slides or using an overhead projector.

Additional Requirements:

In addition to the above requirements, 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. The scientific reports are to be delivered to Fredrik in his office before 5:00 pm on the due date.

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. The FSU bookstore should have them in stock:

• 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 CSIT 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. 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.

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 syllabus page).

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.