STAT/BIOST 550; Fall 2005

STAT/BIOSTAT 550:
Statistical Genetics I; Discrete Mendelian traits

Instructor: Elizabeth Thompson
Time: Tu 8.30-9.50; Th 8.30 -10.20 (NOTE NEW CHANGE)
Place: Bagley 331A

NOTE:

If the room is available, and if no-one has a 10.00 class or other immovable commitment, we will extend the class to 10.20 on Tuesdays. Ooops we could not: NOW THURSDAYS!! In addition to the legitimate Thanksgiving Thursday holiday, we will miss the Tuesday before Thanksgiving (Biostat Symposium) and the final Thursday (I forgot UW's new(ish) Fall system and miscalculated), so it would be nice to make these up these two extra non-class days. If anyone already knows this is not possible for them, please let me know.

Single nucleotide polymorphisms are discrete Mendelian traits!

Here is the course announcement.
Here is an intended course outline: not yet revised for this year.
Here is a draft schedule: only partially revised for this year.

Course information

Grading:

Course will be graded 35% homework, 25% computing labs, 10% for participation in class discussions of homeworks/labs, and 30% final project.
Homeworks or labs will be discussed in class (most) Thursdays. Also, I will drop your lowest-scoring homework in computing your overall homework score.

Office hours

For brief questions, please see me after class -- most days that will be possible for me. If you have a 10.00 class, or need a longer time, please feel free to email for an appointment. Also, feel free to email me questions about course or homework material -- if the question is relevant to many in the class, I may respond to the class email, including your query. If I do that, I may edit your query.

Books

Here is the official UW list for books for this course.

My book might be most useful (except the relevant bits are mostly in notes I'll provide on the web). Weir's book is useful. Ott's book will be very useful for those going on through Stat/Biostat 552, but less so for this first course. Lange's book is there mainly so we can put a library reserve hold on it. It has some very good bits.

Here is the book information for my book.

Email

is good, but is NOT an "instant-messaging" system. I no longer do email from home.
Note my email is thompson@stat or eathomp@u. (I think thompson@u must get quite unhappy, receiving a lot of random emails intended for all the other Thompson's at UW).

Computing

HERE is a link to StatGen computing page. You will need your UWNet ID to access this page.

HERE is some information on how to get yourself set up for the computing for this class.

We will be using some of the software installed on the Biostat linix cluster for Statistical Genetics.
Please get yourself a Biostat account if you do not have one. The Biostat system administrator Jim Hogan has already asked me for a list of full names and UWNet IDs, so I will give him one, if you tell me.

Help on editing file in Unix.

Course materials

Elementary introduction to genetics
These web notes were written for undergraduates, by an undergraduate.
But they may be a useful summary review.

Here is a summary of likelihood ideas and theory (PDF version).

Chapter 1 (PDF) (posted 9/28)
Chapter 2 (PDF) (posted 10/5)
Chapter 3 (PDF) (posted 10/26)
Chapter 4 (PDF) (posted 11/10)

Homeworks and Labs

Week 1: Homework 1 Due after class, Thursday Oct 6. (Note change)
Week 2: Homework 2 and Lab 1 Due after class, Thurs Oct 13.
(Leave #4 of Hwk 2 for next time -- it will be in hwk 3)
Week 3: Homework 3
Week 4: Homework 4 (except 3(iii)) and Lab 2
Week 5: Homework 5
Here is some information about PROJECTS
Week 6: Homework 6 and Lab 3
Week 7: Homework 7
Week 8: Lab 4
Week 9: Homework 8
Week 10: Lab 5

Projects

Projects will be due by 12.20 p.m. on Tuesday Dec 13. (This is the official end time of what would have been the final exam, if we had one.)

StatGen Seminar: BIOSTAT 580B (click here)

Students taking the StatGen core sequence are strongly encouraged to also participate in the StatGen seminar-- a journal club and research presentation seminar that has now been ongoing for over 15 years.

Fall quarter: Dr. Ellen Wijsman is in charge. You will need to email her (wijsman@u) for an entry code. As always, it is Tuesdays at 4.00 p.m., and probably in the Biostat conference room. Winter quarter: Matthew Stephens is in charge (stephens@stat.washington.edu), and for Spring, I will be (thompson@stat.washington.edu).

UW - Statistics: Wednesday, 26-Oct-2005 18:16:00 PDT Contact: Elizabeth Thompson <thompson@stat.washington.edu>