CS 43/143, Spring 2008
Intro to Bioinformatics

Course description

Computation is vital for modern molecular biology, helping scientists to model, predict the behaviors of, and control the molecular machinery of the cell. This course will study algorithmic challenges in analyzing biomolecular sequences (what genes encode an organism, and how are genes related across organisms?), structures (what do the proteins constructed for these genes look like, and what does that tell us about their mechanisms?), and functions (what do these things do, and how do they interact with each other in doing it?). The course is application-driven, but focused on the underlying algorithms and information processing techniques, employing approaches from search, optimization, pattern recognition, and so forth.

For a beautiful visualization of the underlying molecules, see The Inner Life of the Cell, with either musical accompaniment or narration.

Here's a fun little flyer for CS types.

To get a feel for the content (although it will be revised), see the previous version.

Administrative info

Instructor
Chris Bailey-Kellogg | 250 Sudikoff | office hour: after class and by appointment
Teaching Assistant
Priya Natarajan | 205 Sudikoff | office hour: MW 3-4
Announcements and discussion board
Available on Blackboard
Lectures
2A | TuTh 2-3:50 | Wilder 102
Textbook
None required. While there are several great books out there covering some of the material, I haven't found one that comprehensively introduces the topics we'll cover (biomolecular sequence, structure, and function) from a computational perspective. Thus I'll distribute lecture notes and provide references to the literature.
Expected background
This is an introductory course targeted at undergraduate and graduate students in computer science. A background in biology is not required, but students should be interested in catching up quickly on some basic molecular biology and biochemistry. I also very much welcome and encourage the participation of students from the life sciences and other related disciplines. Naturally, a basic understanding of and interest in computational issues is expected. Please contact me to discuss your background and interests.

Coursework and grading

The course seeks to provide broad exposure to some important algorithmic challenges and approaches in bioinformatics. The lectures and readings will provide a fairly general (for a ten-week course) survey of the field. Students will then implement and apply some of the techniques.

Grades are derived from the following:

  • Homeworks: 50%
  • Final project: 25%
  • Midterm exam: 20%
  • Participation: 5%

The homeworks are to be done individually; see the honor code policies below regarding discussion. We encourage students to work in groups for the final project.

Homework and project assignments are to be turned in via Blackboard before class on the due date. Ample time is provided for each assignment, so in general, late submissions will not be accepted. Under extenuating circumstances (prolonged illness, death in the family, etc.), arrangements must be made with the instructor before the due date.

For exceptional work, it is possible to receive extra credit points. Extra credit is tabulated separately from the regular grades on homework and exams, and is used to adjust final grades after the final average is computed. Thus extra credit is always optional, and not doing any extra credit work will never reduce your final grade, even if everyone else in the class does a lot of extra credit.

Honor code

Dartmouth's honor code applies to this course, and academic misconduct policies will be strictly enforced. If you have questions, ask!

You may discuss the homework with other current CS 43/143 students, but your submitted homework must be entirely your own. As part of a discussion, you may show (in person) another student your work. However, your code and any other solutions you submit must be created, written/typed, and documented by you alone. You may not copy anything directly from another student's work. For example, copying a portion of someone else's solution onto a piece of paper would violate the honor code, even if you eventually turn in a different answer. Similarly, e-mailing a portion of your code to another student, or posting it on-line for them to see would violate the honor code. Although all students must create and type in their own code, you may help other students debug their programs once you and they have already written your programs. We do encourage discussion of homework assignments between students, subject to these rules. Note that discussion between two students will be most useful when both students have already made serious attempts to solve the problem on their own.

If you make use of any code that is not your own, you must clearly attribute the source of the code with clear comments in the code that you submit. You do not need to acknowledge discussion with other students on your submitted work. Proper respect for copyright laws as applied to printed materials and software products is subsumed by Dartmouth College's Computing Policies.

The final project may be conducted individually or in a group. Here, collaboration is encouraged. Building on existing code is acceptable, subject to the above comments regarding attribution.

On the quiz, you may not collaborate with, copy from, or otherwise share information with anyone. (You may of course ask questions of the course staff.)

Disabilities

Students with disabilities enrolled in this course and who may need disability-related classroom accommodations are encouraged to make an appointment to see the instructor before the end of the second week of the term. All discussions will remain confidential, although the Student Accessibility Services office may be consulted to discuss appropriate implementation of any accommodation requested.