PLPTH 613
Bioinformatics Applications
Spring 2009
Home page
Schedule
Research project
 K-State Online


Instructor J. C. Nelson
Associate professor
Department of Plant Pathology
4022B Throckmorton
jcn@ksu.edu
2-1359

Class times

Lecture: U 11:30 - 12:20 in Throckmorton 4031 (Willis conference room)
Lab: U 12:30 - 2:30 in Throckmorton 4022A (Plant Pathology computer lab)

Course description
The purpose of this course is to expose you to data sets generated by genomic studies and show how to extract information from them. We will not review the technologies used to generate these data. If you aren't already familiar with sequencing, genotyping, genetic and physical mapping, expression studies, etc., you should take PLPTH 612, Genomics Applications, concurrently. It is closely coupled with 613.

Course organization
Each Thursday, the second weekly lecture of PLPTH 612 will be followed by the lecture and lab session for PLPTH 613. The lecture will explain the principles of the analyses you're about to run. The lab exercises will follow instructions presented on WWW pages linked to the Schedule page.

A problem set will be assigned each week, and will be due by the following Wednesday (the day before the next meeting). All material turned in for problem sets will be in HTML; that is, viewable with a WWW browser. It's easy to write WWW pages, and you will learn how in the first two weeks of class if you don't already know.

Lab exercises may be worked alone or with a partner (these will be assigned, and may differ from week to week). Problem sets must be worked on your own, though consultation with others or the instructor about the principles is generally permissible. Please note that the computer lab is not available to students (except those in Plant Pathology) outside of scheduled hours.

A small research project of your choice will be required (was optional in first offering of course, spring 2009).

Grading will be as follows:
Work
 Total
Problem sets (15)*
 375
Midterm exam
 100
Research project* 50
Final exam*
 100
Discretionary*
 20
Total
 575
* Problem sets turned in late, without advance arrangement with instructor, will be accepted only at instructor's discretion and will earn reduced or no credit.
* Project was optional in 2009 but may be substituted for half of the final exam.
* Discretionary points are awarded based on student's class participation, visible improvement in English writing and document organization, and other evidence of serious effort. The only time they will matter is when the student's score is just below a cutoff (see below).

Letter grade equivalents:
Letter
 % range
 Cutoff
A
 90 - 100
 517
B
 80 - 89
 460
C
 70 - 79
 402
D
 60 - 69
 345

Instructor consulting hours are by arrangement. I'm usually available in my office. Drop-ins are OK but you're not guaranteed to find me free. So it's best to call or e-mail, or to see me after class. When teaching, I consider it the most important work I do, so you'll receive prompt attention.

Cell-phone policy
If during lecture, lab, or office consultation your cell phone rings and/or is answered, or you are seen handling other electronic communication or entertainment gear, you will be asked to leave for the remainder of the session. To avoid distraction to yourself and others, turn off and put away all such devices before entering the classroom, the lab, or my office.