CS 468 Algorithms in Bioinformatics (Fall 2010)

Required Textbook: An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner
Recommended Reference: Introduction to the Design and Analysis of Algorithms, 2/E, by Anany V. Levitin (or any general algorithm book)
Instructor Web site: http://cs.winona.edu/lin/ 

Synopsis: Theory-oriented approach to the design and analysis of contemporary algorithms, and their applications to bioinformatics. This course offers an exposition of the algorithmic principles driving advances in the field of bioinformatics. Data modeling, analysis of algorithm efficiency, algorithm design techniques such as dynamic programming and divide-and-conquer, and machine learning algorithms are discussed in the contexts of genomics and bioinformatics. (Credit will only be given for one of CS 440, CS 468, and CS 469.) Prerequisite: CS 341 Data Structures and BIOL 310 Genetics

Course Objectives and Student Learning Outcomes:
Upon entering CS 468, students should have

• Knowledge of fundamentals of bioinformatics and molecular biology
• Knowledge of data structures such as array, linked list, graph, and tree
• Capability of understanding and implementing algorithms
• Knowledge of proof techniques such as mathematical induction, proof by construction, and proof by contradiction
• Some ability for precise communication and reasoning
• Motivation to study CS and bioinformatics subjects

• Apply algorithmic techniques to solving bioinformatics problems
• Communicate technically with bioinformaticians
• Learn new bioinformatics algorithms from publications
• Understand the power and limitations of algorithms
• Analyze efficiency of algorithms and develop approaches to improve the performance
• Appreciate the contributions of computer science to advances in biomedical research

Grading: Grades are based on three categories: a set of homework assignments (25%), two to three projects (30%), two exams (40%), and participation (5%). The course grade will be based on the total of the categories:
      A: 90% or above, with an average of at least 80% on every grading category
      B: 80% or above, with an average of at least 70% on every grading category
      C: 70% or above, with an average of at least 60% on every grading category
      D: 60% or above
      F: less than 60%.

Homework Policy:
1. Each homework assignment and project assignment is due by the time and date specified on the assignment handout.
2. Non-programming assignments must be typed or written neatly.
3. Late Work: Two late assignments, except for the presentation project, will be accepted without penalty, and a late assignment should be handed in within a week. After the two late assignments, no additional late work will be given credit. The late policy is in place so that students will not be burdened to discuss each personal issue with the instructor. Thus, late assignments should be reserved for these types of situations. If a student has an issue that requires more than two late assignments, it is unlikely they will be successful in the course and they are encouraged to withdraw from the course.
4. Plagiarizing is absolutely prohibited and will result in a grade of F for the course according to the Computer Science Department's Collaboration Policy Form and Illegal Collaboration Policy.

Attendance Policy: You are expected to be present for all class meetings. At a minimum, I expect you to treat each other (and your instructor) politely and with respect. This includes turning off all cell phones (or muting them), participating in class, and arriving in a timely manner. Please remember that personal conversations and using your computer performing tasks unrelated to class during lecture and lab time are distracting to your fellow students.

Student Responsibilities: You are responsible for what goes in the class, including obtaining lecture material, assignments and handouts, turning in assignments, and taking exams.  If you are unable to attend a class meeting, it is your responsibility to obtain class notes, assignments, and extra copies from your study partners, other students, or me; you may turn in assignments early or your study partners may turn them in for you on time.  If, due to extremely unusual circumstances, you are unable to take an exam at the scheduled time, the exam may be rescheduled, but it is your responsibility to arrange this with the instructor in advance as early as possible.

Commitment to Inclusive Excellence
WSU recognizes that our individual differences can deepen our understanding of one another and the world around us, rather than divide us. In this class, people of all ethnicities, genders, religions, ages, sexual orientations, disabilities, socioeconomic backgrounds, regions, and nationalities are strongly encouraged to share their rich array of perspectives and experiences. If you feel your differences may in some way isolate you from WSU's community or if you have a need of any specific accommodations, please speak with the instructor early in the semester about your concerns and what we can do together to help you become an active and engaged member of our class and community. 

Campus Resources
• WSU-Rochester Student & Campus Services, UCR Room SS128, 285-7100, rochsss@winona.edu (www.winona.edu/rochester/)
• WSU Inclusion and Diversity Office, Kryzsko Commons Room 122, 457-5595 (www.winona.edu/culturaldiversity/)
• WSU Disability Resource Center, Maxwell 314, 507-457-2391 (www.winona.edu/disabilityservices/)
• RCTC Counseling Center, UCR Room SS 133, 285-7260 (www.rctc.edu/counseling_career_center/)
• UCR Learning Center, UCR Room AT306, 285-7182 (www.roch.edu/learningcenter/)
• GLBTA Advocate*, 507-457-5330
• Advising and Retention, Maxwell 314, 507-457-5878 (www.winona.edu/advising/)

Details about Campus Resources
• Two good places to help you find resources of all kinds are the WSU-Rochester Student & Campus Services Office and the WSU Inclusion and Diversity Office. Both offices are dedicated to helping students of all races, ethnicities, economic backgrounds, nationalities, and sexual orientations. They can facilitate tutoring and point you to a wide range of resources. The WSU-R Student & Campus Services Office is located in Room SS128 on the UCR campus and can be reached at 285-7100. The WSU Inclusion and Diversity Office is in Kryzsko Commons Room 122, and they can be reached at 457-5595.
• If you have a disability, the WSU Disability Resource Center (DRC) can document it for your professors and facilitate accommodation. Their office is on the Winona campus in Maxwell Hall and they can be reached at 457-2391. If you have a documented disability that requires accommodation, please let me know as soon as possible. If you suspect you may have a disability, you are encouraged to contact the DRC as soon as possible.
• College can be very stressful. Counselors are available in Winona and through partnership with RCTC on the UCR campus to help you with a wide range of difficulties, ranging from sexual assault, depression, and grief after the loss of a loved one to stress management, anxiety, general adjustment to college, and many others. WSU counselors in Winona are located in Wabasha Hall 220 and they can be reached at 457-5330. The RCTC Counseling Center is located in SS 133 and can be reached at 285-7260.
• For help with writing and the development of papers on the WSU-Rochester campus, contact the UCR Learning Center in AT306 or call 285-7182.
• The GLBTA Advocate is responsible for documenting homophobic incidents on campus and working with the appropriate channels to get these incidents resolved. In addition, the advocate can direct people to GLBT resources. * Contact the WSU Counseling Center for the name and number of the current GLBTA Advocate (Integrated Wellness Center 222, 507-457-5330).

UCR Learning Center
The UCR Learning Center (LC) provides learning support for everyone on campus: developmental students, regular students, honors students, WSU students, all the way to doctoral students and faculty members. It offers tutoring in math, stats, computer applications, writing, resume writing, MLA or APA format, science, reading, speech, and many other academic disciplines. It also offers test proctoring. It is NOT a correction service or a drop-off service. In other words, the LC personnel will not fix your assignments or correct things. They will, however, happily help you learn the material in a way that makes sense for you! Please be sure to sign in at the computer sign-in terminal every time you enter the LC. This data provides the necessary information to assure that the LC remains funded.