|3/3||Cristina's office hours on Thursday 3/5 will be moved to 3:30-4:30.|
|2/26||Problem Set 4 has been posted.|
|2/21||On PS3 problem 4(d), you need to provide a tree where your algorithm cannot do better than O(n^2), regardless of the order the nodes are chosen.|
|2/11||Problem Set 3 has been posted.|
|1/30||There will be no problem session this Friday, January 30.|
|1/28||Problem Set 2 has been posted.|
|1/20||There was a typo in the Problem Set 1 due date - it is due Wednesday, January 28 at the beginning of class.|
|1/20||Students planning to scribe a lecture should email the staff list with your top 3 choices (in order). These will be assigned on a first come, first serve basis.|
|1/20||Students looking for homework groups should email the staff list ASAP and/or attend the problem session this Friday, January 23.|
|1/14||Problem Set 1 has been posted.|
|1/14||Locations and times have been finalized for all staff office hours and the problem session. The first problem session will be this Friday, January 16.|
|1/14||The staff mailing list ude.drofnats.stsil@ffats-9080niw-262sc (written backwards) has been created. Please use this list rather than emailing course staff individually.|
CS161: Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts.
Durbin, Eddy, Krogh, Mitchison "Biological Sequence Analysis"
Gusfield "Algorithms on Strings, Trees, and Sequences"
Homework. Course will be graded based on the homeworks, NO FINAL. The course will have four challenging problem sets of equal size and grading weight. These must be handed in at the beginning of class on the due date, which will usually be two weeks after they are handed out. Recognizing that students may face unusual circumstances and require some flexibility in the course of the quarter, each student will have a total of three free late days (weekends are NOT counted) to use as s/he sees fit. Once these late days are exhausted, any homework turned in late will be penalized at the rate of 20% per late day (or fraction thereof). Under no circumstances will a homework be accepted more than three days after its due date.
Late homeworks should be turned in to a member of the course staff, or, if none are available, placed under the door of S266 Clark Center. You must write the time and date of submission on the assignment. It is an honor code violation to write down the wrong time. Students with biological and computational backgrounds are encouraged to work together.
Scribing. Optionally, a student can scribe one lecture. Lecture notes will be due one week after the lecture date, and the grade on the lecture notes will substitute the two lowest-scoring problems in the homeworks. To ensure even coverage of the lectures, please sign up to scribe beforehand with one of the course staff.
Students may discuss and work on problems in groups of at most three people but must write up their own solutions. A student can be part of at most one group. If a student works individually, then the worst problem per problem set will be dropped. When writing up the solutions, students should write the names of people with whom they discussed the assignment. Also, when writing up the solutions students should not use written notes from group work.
Students are expected not to look at the solutions from previous years. Copying or intentionally refering to solutions from previous years will be considered an honor code violation.
Problem Sessions (optional): Friday 3:00 - 4:00pm in Clark S361
Office: Clark S266
Office hours: Mon 1:30 - 2:30 pm
Phone: (650) 723-3334
Email: ude.drofnats@mifares (written backwards to avoid spam)
Office: Clark S256
Office hours: Tue 1:00 - 3:00pm, Wed 1:30 - 2:30 pm
Phone: (650) 725-6503
Office: Gates B26A
Office hours: Mon 4:30 - 5:30 pm, Thu 1:00 - 2:00 pm
Phone: (650) 723-6319