CSCI1950L: Algorithmic Foundations of Computational Biology

Semester:

Spring 2011

Schedule:

Tuesdays and Thursdays 2:30-3:50pm (K)

Location:

CIT Swig Boardroom

People:

Office Hours:

Course Organization

People (cs195ltas@cs.brown.edu)

Professor

Prof. Sorin Istrail
401-863-6196

Teaching Assistants

Office Hours (tentative)

  • James: Tuesday 5-7pm in Fishbowl CIT 244
  • Sorin: Monday 4:30-5:30pm in CIT 523 or by appointment (email Sorin Sorin_Istrail at brown dot edu and cc Angel Murakami akm at cs dot brown dot edu)
  • Derek: Wednesday 12-2pm in Fishbowl CIT 244 or by appointment

Contacting Us

To schedule an appointment with Sorin, contact him directly via the above email.

Please use the following email address to ask questions of the TAs, for help with homework, or for any other purposes: cs195ltas@cs.brown.edu

Structure of the Course

(tentative for now)

Homework

Homeworks will be assigned each Thursday and will be due at 2:30pm the following Thursday. Towards the second half of the course, homeworks will be assigned less frequently but will also be more involved, typically spanning two weeks instead of one. At most two homework assignments may be turned in late during the semester and late submissions are subject to penalties.

Programming may only be done in languages accepted by the TAs. We are very flexible, as long as it will run on a department computer (email the TAs regarding any questions on this).

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 when available. Project presentations will assigned at a date TBA, but are expected to start sometime during the second month.

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 24 hours to complete them. Their dates will be determined later in the course.

Collaboration Policy

VERY IMPORTANT: You are expected to complete homework assignments individually, with no assistance from other students. Please do not discuss problems or share answers with any other student. Questions regarding the homeworks should be addressed to the TAs or the professor. The same policy applies to the midterm and final exams, with strict adherence demanded.

All assignments are open-note, open-book, and you may make reference to Internet resources. However, the course staff has experienced problems with students deliberately or inadvertently integrating snippets of solutions or code lifted from the Internet. Plagiarism is strictly not allowed. Please do not search the Internet for inspiration to solve a problem, because you may consciously or subconsciously borrow ideas from others. We may check your submissions against the MOSS (Measure of Software Similarity) database to find plagiarism in your code.

(Note that there will be occasional exceptions, such as assigned groupwork, or for support code which helps you parse input into your program. In that case, the allowed collaboration will be made explicit in the assignment.)

Grading

  • Homeworks – 40%
  • Class participation (discussion, presentations, reading) – 10%
  • 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/csci1950-l/

Books

There are no mandatory textbooks for the course. Instead the professor will provide regular readings which you are expected to do as part of your participation grade.

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 following options:

  • For CS theory-oriented students, a more in-depth survey of an algorithm or topic that was discussed in class.
  • Systems-oriented students will work with the professor to define a programming project.
  • Life sciences students will complete an assignment in their area of expertise which is equivalent to a programming project in time/difficulty.

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