Announcements

• (12/4) There will be a Final Exam study session tonight, 12/4, in FB007 from 5:30-7:00pm.
• (11/30) Kemal: My office hours on Monday 12/1 will be between 12-5pm
• (11/18) I modified the programming part of problem set #4 to exclude any strings containing an 'N'.
• (11/6) I have posted a new version of the ReadFasta() function which is much faster on windows machines.
• (10/10) The midterm will be held on Oct 15. It will be short-answer format. It is open-book, open notes, and closed computer or otehr network connected devices (phones, tablets, readers, etc.).
• (10/10) A study session for the midterm with be held on Monday, Oct 14, in FB008 from 5pm-7pm
• (10/7) At 5pm I uploaded a new version of breakpointReversalSort.txt, that fixes a bug. It should not impact the anaswer to the programming problem of PS2 however.
• (10/7) I have clarified the inputs to the programming problem (added extension to the rght-end of the permutations). 
• (10/7) For programming problem of PS2 submit both the code and the outputs for the given examples.
• (10/7) Leonard will hold extra office hours on 10/7 (today) from 3pm to 5pm in SN311
• (10/3) The midterm will be held on 10/15, as shown in the schedule, not 10/10 as appears in the syllabus.
• (10/1) I moved the due date for Homework 2 to 10/8.
• (9/19) There was a value missing in the input_1 file of the programming problem. It has now been fixed. If you solved the problem using an earlier version, you should reconsider your answers with the new version.
• (9/16) Kemal will hold office hours during classtime on Tuesday 9/24
• (9/16) Kemal will hold extra office hours for this week on Friday (9/20) from 11am-2pm.
• (9/12) I have moved the due date for Problem Set #1 to allow time for clarification.
• (9/10) We will hold a Python Tutorial at 5pm on Wednesday (9/11) in FB-007
• (9/3) Problem Set #1 is now posted. I may change the due date, stay posted.
• (8/26) I fixed the calendar so that fall break fell in the right place.
• The first lecture will be held on August 20, 2013. The course syllabus can be found here.

Course Description

Computational methods are fueling a revolution in the biological sciences. Computers are already nearly as indispensable as microscopes for analyzing and interpreting biological data. As a result, two new multidisciplinary fields, bioinformatics and computational biology, have emerged. This course will explore the computational methods and algorithmic principles driving this revolution. It will cover basic topics in molecular biology, genetics, and proteomics. The course also addresses basic computational theory and algorithms including asymptotic notation, recursion, divide-and-conquer approaches, graph algorithms, dynamic programming, and greedy algorithms. These fundamental concepts from computer science will be taught within the context of motivating problems drawn from contemporary biology. Example biological topics include sequence alignment, motif finding, gene rearrangement, DNA sequencing, protein peptide sequencing, phylogeny, and gene expression analysis.

This course is suitable for both computer science and biology students at both undergraduate and graduate levels, and thus is co-listed as both COMP590-87 and COMP790-87. Students who wish to take this course should have some programming experience in a modern language. Knowledge of data structures, algorithm design, and biology is helpful but not required. There will be 6 problem sets with short programming assignments, a midterm, and a final exam.

A syllabus for this offering of Comp555 can be downloaded from here.

Book, Course Information, and Prerequisites

Course Instructors

Schedule