CS5890 Bioinformatics: Problems and Solutions

June 12- Aug 4, 2006

Credits: 3

Time: MW 12:10-14:20, F 12:10-1:10

Place: Old Main 117

Instructors: 

Nick Flann, Computer Science

Nick.flann@usu.edu 797-2432

Sean Johnson, Biochemistry

Sean@cc.usu.edu 797-2089

Mark Miller, Biology

Mark.Miller@usu.edu 797-7609

John Stevens, Math and Statistics

John.R.Stevens@usu.edu 797-2818

Course Goals:

• Become familiar with several bioinformatics problems

Computational analysis of human disease mutations

Gene finding

Gene expression analysis

Protein structure analysis

Modeling regulatory networks and cellular pattern development

• Understand the approaches that are used to address these problems

Learning Outcome:

• Be able to identify and utilize suitable bioinformatics resources to solve the  problems covered by the course

Poster Template:

• Here are two poster templates to choose from. Posters must follow one of these templates and be 42 in. tall and 60in wide.
• Template1
• Template2

Grading:

Work	5890 Students	6890 Students
Project progress reports	30	30
Final project archive	10	10
Project poster presentation	30	30
Individual class participation	10	10
Individual project contribution	10	10
Individual written report	0	30
Total	90	120

Project:

            Each of the four instructors will introduce one topic. Students registered in the class will be divided into four groups. Groups will be assigned topics based on group preferences, skills and instructor judgment. Once the groups are formed, they will work together to investigate the topic, mentored by one instructor. Each week each group will make a progress report to the class as whole, detailing how their project has advanced and their plans for the next week. Students in other groups will be encouraged to become knowledgeable of each class project and offer criticism and ask questions during the progress reports. Student involvement is to be encouraged.

Each week each group will meet individually with their mentor to discuss project progress and plan for the group progress report. There will be a poster session on Aug 1, where each group will present the results of their projects as a poster.

Course Website:

            The website for this course is http://www.cs.usu.edu/~flann/CS5890/.

Textbook: None

Cheating Policy:

            Please be aware of the department cheating policy . No cheating is tolerated in this class.

Class Schedule:

Date	Day	Topic	Instructor	Slides
June 11	M	Introduction to genetics/genomics	Mark Miller	PDF
June 13	W	Introduction to bioinformatics/ Project topic	John Stevens	PDF
June 15	F	Project topic (2 hour special)	Sean Johnson	PDF
June 18	M	Project topic	Mark Miller	PDF
June 20	W	Project topic	Nick Flann	PDF
June 22	F	Project team formation	All
June 25	M	Each project group meet with mentor	All
June 27	W	Group presentations	All
June 29	F	Office hours
July 2	M	Each project group meet with mentor	All
July 4	W	National Holiday
July 6	F	Lecture	Nick Flann	PDF
July 9	M	Lectures	John Stevens & Sean Johnson	Johnson Stevens-PDF Stevens-data
July 11	W	Group presentations	All
July 13	F	Lecture	Mark Miller
July 16	M	Each project group meets with mentor	All
July 18	W	Group presentations	All
July 20	F	Office hours
July 23	M	Each project group meets with mentor	All
July 25	W	Group presentations	All
July 27	F	Office hours
July 30	M	Each project group meets with mentor	All
Aug 1	W	Poster session

Project Groups

Project	Students	Supervisor
Gene expression analysis		John Stevens
Computational analyses of human disease mutations		Mark Miller
Protein structure analysis		Sean Johnson
Developmental modeling		Nick Flann

Project Group Presentations

Project Groups	John Stevens	Mark Miller	Sean Johnson	Nick Flann
June 27	PDF	PDF	PDF	PDF
July 11	PDF	PDF		PDF
July 18	PDF	PDF		PDF
July 25
August 1st