CS196-1: Algorithmic Foundations of Computational Biology

Course Organization [PDF]

People (cs196-1tas@cs.brown.edu)

Professor

Prof. Sorin Istrail
401-863-6196

Teaching Assistants

Office Hours

  • Sorin –
  • Sanjay –
  • Brendan –
  • Long –
  • Rohan –

Contacting Us

To schedule an appointment with Sorin,

Please use the following email address to set up appointments, ask questions or for any other purposes: cs196-1tas@cs.brown.edu

Structure of the Course

(tentative for now)

Homework

Homeworks will be assigned each Tuesday and will be due at 11:59pm the following Tuesday. Towards the second half of the courses, homeworks will be assigned less frequently but will also be more involved, typically spanning two weeks instead of one. Homeworks must be turned in on time and late submissions may be subject to penalties.

Programming may only be done in languages accepted by the TAs.

Biology and medical students will get special homework to compensate for the programming assignments in the homework.

Projects

The list of suggested projects for biologist and grad student credit will be listed on the project page. Project presentations will be given on dates decided at the end of the semester.

Midterm and Final

The midterm and final will be modeled after the homework assignments. They will both be take-home, open-book and you will have 1 day to complete them. Their dates will be determined later in the course.

Grading

  • Homeworks – 50%
  • Midterm – 25%
  • Final – 25%

Course Resources

Web Site

Nearly everything you will need will be made available through the course web site, including TA notes, slides, homework assignments, tests, etc. Please check the web site regularly. The web site is located at: http://www.cs.brown.edu/courses/cs196-1/

Books

TBA

Prerequisites

The course is designed for graduate students and upper-level undergraduates. It is also open to Computer Science and Math students, as well as biological and medical students. Since the class will be comprised of students with a diverse background, homework and tests will involve general questions for all students as well as more in-depth questions, which you will be able to choose from in accordance with your particular background. While there are no formal prerequisites for the courses, you should have a strong background in at least one of these two areas. Please contact the professor if you are unclear as to whether you have the necessary prerequisites for the course.

200-level Credit

Graduate students will have the option of obtaining 200-level credit for the course by completing one of the two following options:

  • For theory-oriented students, a more in-depth survey of a topic that was discussed in class.
  • Systems-oriented students will work with the professor to define a programming project.

All graduate-level credit projects must be approved by the professor.

Collaboration Policy

You may discuss the homework problems with other students or use other resources such as textbooks or the Internet. However, you must not obtain answers directly from anyone else. All homeworks will be submitted individually. The midterm and final are not to be discussed with other students.