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Idaho Math/Bio 563                                    WSU Math 563 Bio 566

Mathematical Genetics

University of IdahoWashington State University

Fall 2011


The first  and  homework assignment  is  due Sept. 26.
The second homework assignment is  due Oct. 3.
The third homework assignment is due Oct. 17
The fourth homework assignment is due Oct.  31
The fifth homework assignment is due Nov. 7
The sixth homework assignment is due Nov.  16
The seventh  homework assignment is due  Nov. 30


Student projects and reading materials are posted on the syllabus.


Coalescent Theory Slides
Approximate Bayesian Computation
Homework 1

Homework 2

Homework 3

Homework 4

Homework 5

Homework 6

Homework 7


 
Syllabus, Reading
Assignments and Homework


Handouts


Textbooks


REQUIRED
Evolutionary Theory
Mathematical and Conceptual Foundations
by Sean Rice

A list of typos
for Rice



Suggested reference books

Gene Genealogies, Variation and Evolution
by Hein, Schierup and Wiuf


Coalescent Theory, An Introduction
by John Wakeley

UI Professor:
Paul Joyce 
Departments of Mathematics and Statistics
Initiative for Bioinformatics and Computational
Biology (IBEST) 

University of Idaho

WSU Professor:

Richard Gomulkiewicz 

School of Biological Sciences


      Washington State University
E-mail:
joyce@uidaho.edu

Office

Brink Hall 413 

Phone: 

885-6338 

Office Hours for Paul Joyce:
By appointment
E-mail: 
gomulki@wsu.edu

Office:

 Eastlick 391


Phone:

335-2527

Office Hours for Richard Gomulkiewicz:
By appointment.

Class Meeting

Wednesday
5:10- 6:25 pm

 TLC 122
UI CAMPUS

Class Meeting

Monday
5:10:-6:25 pm
TODD 307
WSU CAMPUS



 


 

Course Goals
(1) Gain exposure to, and experience with, major topics and methods in mathematical genetics; 

(2) Survey classical and contemporary literature in mathematical genetics.
 
 

Course format:

We plan to achieve the goals of the course through a series of instructor led “workshops” topics in mathematical genetics during the first part of the course and student led group discussions during the second part of the course.  One or two readings will usually be assigned per topic: one for background and a second for discussion. 

 For workshops, an instructor will briefly motivate the topic, outline the analyses, and summarize the main results.  The class will then work through the reading(s) as a group, stopping to clarify steps, methods, or concepts that are ambiguous.  Ideally, students who understand a step/method/concept will do the clarifying.  Of course, the instructors will help regulate the flow of discussion and contribute lucid explanations as necessary!  The instructors will also suggest homework problems which all students will be expected to attempt.  For this workshop format to succeed, it is critical that every student works to understand the readings prior to class.  If, in the course of reading the material, you don’t understand something (e..g., a term, concept, manipulation, or technique) make a note of it and go through the remaining material as best you can.  Be sure to bring your notes to class.

Student-led group discussions will cover topics chosen by students (topics—which may involve original research—must be pre-approved by the instructors).  Leaders should prepare handouts and readings that their fellow students will read prior to the discussion.
 
 

 










Internet Resources

Java Demonstrations of
the coalescent Process


Lamarc

Genetree

A recombination program

List of phylogenetic software
by Joe Felsenstein

Grading Criteria

Half of the grade in this course will based on the quality of a student planned and executed group discussion during the second part of the course.  The other half of your grade will be based on in-class participation.  Your participation grade will be based on (a) attendance [10%], (b) the contributions you make during discussions (including asking and answering questions, and making thoughtful comments) [10%], and (c) attempting and solving any assigned homework problems [30%].


 

Reading  Assignments: Readings will be assigned from current and classical literature.  You will be expected to  have read the assigned paper and participate in discussing the material.  You will be assigned four or five questions about the reading.  You will be required to answer each of the questions. 
 

 Web Resources

To your left are a number of interesting web sites with information and computer software.   If you find any  web sites that you feel would be of interest to your instructors and/or fellow students, let me know (joyce@uidaho.edu).  I would be happy to post them.


Parking information:

You may park for free after 5:00 pm on most lots at both WSU and UI.  For more information about UI parking visit<>  http://www.uidaho.edu/parking/parkingenforcementschedule


For information about WSU parking visit
http://www.parking.wsu.edu/


WSU Academic Integrity Statement:

Academic dishonesty will not be tolerated in this course. Any student who acts unethically will be given an F for the course and referred to the Office of Student Conduct.  For information, see:   http://www.conduct.wsu.edu/default.asp?PageID=343

http://www.wsulibs.wsu.edu/plagiarism/main.html

 

WSU Students with Disabilities:

Reasonable accommodations are available for students with a documented disability. If you have a disability and may need accommodations to fully participate in this class, please visit the Disability Resource Center (DRC). All accommodations MUST be approved through the DRC (Washington Building, Room 217). Please stop by or call 509-335-3417 to make an appointment with a disability specialist.

Campus Safety/Emergency Information:

      In the interest of campus safety and emergency procedures, please become familiar with the information available on the WSU-provided websites. Also, please register your emergency contact information at myWSU.

      http://safetyplan.wsu.edu, Campus Safety Plan

      http://oem.wsu.edu/emergencies, Emergency management web site

      http://alert.wsu.edu, WSU Alert site.