CS6890 Bioinformatics: Problems and Solutions

June 12- July 30 , 2008

Credits: 3

Time: MW 11:00, F 11:00

Place: Library 302

Instructors: 

Nick Flann, Computer Science

Nick.flann@usu.edu 797-2432

Course Goals:

• Become familiar with how cellular automata can model complex biological processes
• Understand selected biological modeling problems such as development of tissue, patterns and cancer

• Understand how cellular automata models are implemented
• Understand types of cellular automata
• Develop skills in team work, meeting deadlines and making scientific presentations

Learning Outcome:

• Be able to identify biological problems and utilize cellular automata to answer scientific questions

Final report :

• Each student in the class must submitt a 4-10 page report describing their project by August 4th at midnight. The report provides an opportunity for the student to demonstrate their knowledge of their team's project and outline their individual contributions. The report should include the following: Introduction: the problem solved and its significance to biology is explained at a high level; Approach: the algorithms, methods and code is described in detail. Results: pick a few different examples of the system running which best illustrate the power and flexibility of the approach. The report should also include a summary and conclusions section and at least 3 references.

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

Demonstration project ideas :

• click here to see a description of some biological demonstration projects that can be easily implemented with the integrated project..

GUI Code :

• click here to download an old project showing how to use a Canvas to display the CA models .

Vitruvian Code :

• click here to download the service based intergration code.
• interface design document

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:

            There will be four project topics introduced. 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 the 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 the instructor 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/summer2008.

Links:

http://people.ee.ethz.ch/~reint/schelling/

http://www.cmth.bnl.gov/~maslov/Sandpile.htm
http://www.math.com/students/wonders/life/life.html

Many great demos of different cellular automaton systems using mathematica. To experiment with the demonstrations, you will need to download and install the mathematica player.

Here are two papers that we will be using for our projects:

Cellular Potts model

Cancer Tumor models

Optional Textbook: Cellular Automaton Modeling of Biological Pattern Formation by Andreas Deutsch and Sabine Dormann

Cheating Policy:

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

Class Schedule:

Date	Day	Topic	Slides
June 11	W	Introduction to cellular automaton	PDF
June 13	F	Experiments with cellular automaton
June 16	M	Developmental models	PDF
June 18	W	Project topics
June 20	F	Project topics
June 23	F	Project team formation
June 25	W	Each project group meet with instructor
June 25	W	Group presentations
June 27	F	Office hours
June 30	M	Project teams work on project
July 2	W	Project teams work on project
July 4	F	National Holiday
July 7	M	Lectures
July 9	W	Group presentations
July 11	F	Office hours
July 14	M	Each project group meets with instructor
July 16	W	Group presentations
July 18	F	Office hours
July 21	M	Each project group meets with instructor
July 23	W	Group presentations
July 25	F	Office hours
July 28	M	Each project group meets with instructor
July 30	W	Poster session

Project Groups

Project	Project	Students	Supervisor
one	Cellular Potts Model cells		Nick Flann
two	Cellular Potts Model parallel		Nick Flann
three	Tumor growth		Nick Flann
four	Pattern development		Nick Flann

Project Group Presentations

Project Groups	one	two	three	four
June 25
July 9
July 16
July 23
July 30