math5610

MATH 5610: Computational Biology -- Syllabus (Spring 2005)

Tues/Thurs, 5:30-6:45 p.m., Science Bldg., Room 113
www-math.cudenver.edu/~billups/courses/5610_S05.html

Prerequisites: Linear algebra, differential equations, probability, some programming experience. Some knowledge of graph theory will be helpful, but is not required.

Textbook: Fundamental Concepts of Bioinformatics, by Dan E. Krane and Michael L. Raymer, Benjamin Cummings, 2003.

Instructor: Stephen C. Billups
Office: CU-Denver Bldg., Rm 607, (303) 556-4814 Office Hours: TR 3-4, (or by appointment) Stephen.Billups@cudenver.edu www-math.cudenver.edu/~billups/

Assistant: Christiaan van Woudenberg
Office: CU-Denver Bldg., Rm 653, Office Hours: TBA Christiaan@xiaan.com

Overview: This course is an introduction to computational problems in molecular biology. We will cover enough topics to give a broad overview of bioinformatics, and shall also go into depth on a smaller number of topics.

Grading: Problem sets (40%), midterm exam (10%), short presentation (5%), project (30%), take-home final (15%)..

Problem sets: Problem sets will be assigned throughout the semester. Some of these problem sets will involve using computers. You will always have at least a week to complete any homework assignment. These problem sets will test your understanding of the concepts presented in class (harder questions), and introduce some concepts that we won't be able to cover in class (easier questions), but will come with adequate supporting materials to answer the question(s). Late homeworks will be assessed a 20% penalty, but will not be accepted more that 48 hours late.

Midterm Exam: This will be a closed book in-class exam. (Thursday, March 10)

Short Presentation: You will give a short (5-10 minutes, depending on class size) presentation on a topic related to computational biology. I will provide a list of topics for you to choose from. Your presentation should give a clear description of the topic and how it relates to computational biology.
Project: You will do a term project on a topic of your choosing. I will provide a list of possible project topics early in the semester, but you are encouraged to devise your own. Start thinking about this early! The project will include the following deliverables:

Project Proposal: Due Tuesday, March 8 before class.
Draft Report: Due Tuesday, April 19 before class. (Must be double spaced).
Final Report: Due Friday, May 6, at noon.

Final: This will be a take-home exam, which will be given out on May 3, and will be due May 13 at noon.

Other Requirements:

Computer usage: You will need an account on "math", and will need to use MATLAB and LaTeX.

Important Dates:

March 8	Project proposal due
March 10	Midterm
March 19-27	Spring break--no class
April 19	Draft report due
May 6	Final report due
May 13	Take-home final due

Spring 2005 Registration Deadlines and Responsibilities for CLAS Students

CLAS students must always have an accurate mailing and e-mail address:  http:/www.cudenver.edu/registrar.

Students are responsible for completing financial arrangements with financial aid, family, scholarships

INCOMPLETE GRADES (IW/IF):   Incomplete grades (IW or IF) are not granted for low academic performance.  To be eligible for an Incomplete grade, students must (1) successfully complete 75 percent of the course, (2) have special circumstances (verification may be required) that preclude the student from attending class and completing graded assignments, and (3) make arrangements to complete missing assignments with the original instructor.  A CLAS Course Completion agreement is strongly suggested.

    12 January (5:00 pm)   Payment plan deadline for students registering by 17 December 2004.   Students not on financial aid are administratively disenrolled for non-payment.
20 January   Last day to be added to the wait-list for a closed course.
24 January – 1 February   Students are responsible for verifying an accurate Spring 2005 registration via SMART.
27 January (midnight) Last day to add courses via the web SMART system.
2 February (5:00 pm) Last day to add 16-week structured courses. Treated as an absolute deadline.   The 2 Feb deadline does not apply to independent study, internships, and late-starting modular courses.
2 February (5:00 pm) Last day to drop a Spring 2005 course for tuition refund and no transcript notation.
2 February   Last day for undergraduates and graduates to apply for May, 2005 graduation.
4 April   Last day to drop a Spring 2005 course without college approval.
15 April    Last day to drop a Spring 2005 course for CLAS students. Treated as an absolute deadline.

Consult the Academic Calendar for details on registration/payment deadlines: http://www.cudenver.edu/registrar