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

Instructor: Elizabeth Thompson
Time: Tu, Thur 8.30-9.50
Place: EEB 025

SOME OF THE INFORMATION ON THIS PAGE MAY NOT BE UPDATED FOR 2007

Single nucleotide polymorphisms are discrete Mendelian traits!

Here is the course announcement.
Here is a draft schedule: only partially updated for this year.
The draft schedule is usually the first place I update and check links.

PLEASE LET ME KNOW ABOUT ANY NON-WORKING LINKS THAT YOU BELIEVE SHOULD BE WORKING.

Course information

Grading:

Office hours

Books

See also the course announcement.

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.

Note I have copies of my book available, courtesy of the UW 2007 Statistical Genetics Summer Institute. Don't go pay the bookstore $40.00 !! Here is the (old) book information for my book.

Email

is good, but is NOT an "instant-messaging" system. I no longer do email from home.
Note my preferred email is 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 for Statistical Genetics installed on the Biostat linux cluster.
I will provide a list of full names and UWNet IDs to the Biostat systems administrator, after the first day of class.
If you miss this list, please get yourself a Biostat account if you do not have one.

Here are some bits and pices of possible help: they are also linked in the lab docs:

• Copying and editing files or use this older vi editor
• Strange problems with files out of DOS (Notepad, for example)
• Problems with ssh, or graphics windows -- soon!

Course materials

THESE ARE NOW ALL UPDATED

• 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).
  We will cover this stuff in class, but this is a more detailed general summary than is in the notes.
• Here is a note about expectations
  which may be helpful to those with less probability and statistics background (posted 10/14/2007).
• Chapter 1 (PDF) (posted 9/23/2007)
• Chapter 2 (PDF) (posted 10/14/2007)
• Chapter 3 (PDF) (posted 10/29/2007)
• Chapter 4 (PDF) (posted 11/18/2007)

Homeworks and Labs

• Week 1: Homework 1 (Posted 9/20/2007). Due after class, Thursday Oct 4.
  
• Week 2: Homework 2 (Posted 10/01/2007) and Lab 1 (Checked on abacus, 9/21/2007).
  Due after class, Thurs Oct 11.
  
• Week 3: Homework 3 (Draft 10/01/2007: finalized (reduced!) 10/10/2007).
  Due after class, Thurs Oct 18.
  
• Week 4: Homework 4 (posted 10/14/2007) and Lab 2(Checked on abacus and posted 10/10/2007)
  Due after class, Thurs Oct 25.
• Week 5: Homework 5 (posted 10/19, confirmed 10/24/2007) Due after class, Thurs Nov 1.
  A good week to start thinking about your final project
• Week 6: Lab 3 (Checked on abacus and posted 10/24/2007)
  No homework this week, but turn in a piece of paper with some idea of what you want to read/do for your project.
• Week 7: Homework 6 (posted 11/02/2007). Due after class, Thurs Nov 15.
  
• Week 8: Lab 4 (Checked on abacus and posted 11/04/2007; text may be clarified).
  Due by email before Thanksgiving (Nov 22).
• Week 9: Homework 7 Due after class, Thurs Nov 29.
  
• Week 10: Homework 8 (posted 11/26/2007) and Lab 5 (posted 11/21/2007) Due after class, Thurs Dec 6.
  
• Due by Dec 11: Final Project

Projects

Lab documents

• Help on editing file in Unix: posted 9/21/2007.
• Copying and editing files.
• Strange problems with files out of DOS (Notepad, for example)
• Lab 1: (posted 9/21/2007) MORGAN/pedcheck
• Lab 2: ( posted 10/10/2007) Pedfiddler
• Lab 3: ( posted 10/24/2007) PHASE and MORGAN/kin
• Lab 4 (Checked on abacus and posted 11/04/2007; text may be clarified). MORGAN/ibddrop and lm_auto
  
• Lab 5: (posted 11/21/2007) Merlin multipoint lodscores (Hopefully final; let me know of problems.)

StatGen Seminar: BIOSTAT 580B (click here)

Fall quarter: Dr. Bruce Weir is in charge. Entry codes are no longer required, but new participants should email him (bsweir@u). As always, it is Tuesdays at 4.00 p.m., and probably in the Biostat conference room.