This course introduces the foundations of algorithmic techniques and analysis, as motivated by biological problems. Topics include dynamic programming, tree and graph algorithms, sequence analysis, hidden markov models. Motivations include sequence alignment, motif finding, gene prediction, and phylogeny.
D or better in BCB 5250.
At the conclusion of this course, students should be able to:
Class: TuTh from 2:15-3:30pm, Room 106 in Ritter Hall
Office Hours: Tuesday 3:15-4:15, Wednesday 2-3pm, or by appointment, in 301 Ritter Hall
The primary text for this class will be An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner.
In addition, we will use lecture notes by Ben Langmead, available on his teaching materials page.
I will post references in the schedule dailty with pointers to the source material, either from these two sources or (occasionally) from some other reference.
Outside of office hours and lectures, email is usually the easiest way to get ahold of me with questions. I will check email several times throughout the work day, and will also check email once per evening to answer questions and resolve issues. Email contact over the weekend will likely be more sporadic, although I will be sure to check at least once.
Laptops and other electronic devices are unnecessary for most of this course, and are frequently a distraction to other students in lecture. Since you are unlikely to need a computer during lecture, please do not bring laptops or other electronics for use in class.
Also, please ensure that your cell phone is set to vibrate or silent during lecture, and do not send text messages of any kind.
There will be homework due regularly throughout the semester, with a total (roughly) 8 problems sets. Most will be written problem sets, due on paper at the start of class.
For all homeworks, you are allowed to required to submit individual solutions. However, I encourage all of you to work with another student, as the best way to learn this material is to discuss and problem solve in a small group. Verbatim copying (from another student or from the internet) is forbidden, so please be sure to write up your solutions on your own. (A good rule of thumb is to take notes when working in a group, but then write them up later solo without the notes, and just reference the notes if you forget any details.)
In addition to problem sets, I will also have essay assignments throughout the semester. Typically these will be 1-2 pages papers, often asking you to summarize a paper or describe some reading that goes beyond course material. These will be due on paper, at the start of class.
Letter grades will be based on each students overall percentage of awarded points according to the following formula.
Any modification to this scale at the end of the year will be in favor of the students. That is we may later decide to award an A to a student who is slightly below the cutoff, but we certainly will not deny an A from someone who is above the cutoff.
No matter what curve I impose, I maintain that the minimum passing grade for this class is a 50% - so if your average is lower than that, you will fail this class.
In general, extra credit will not be assigned in this class. The homework assignments provided will be challenging enough for everyone, so I would like for students to focus on the assignments provided.
Upon occasion (and solely at the instructor's discretion), some small extra credit activities may be included, either by announcement in class or as part of an assignment. Please keep in mind that the extra credit is unlikely to significantly affect your grade; if you are concerned about your final grade, it is much better to focus your energy on the regular assignment. Extra credit is solely designed to provide an opportunity to students who wish to explore the topics further.
Late homework will suffer a penalty of 10% for every hour they are late. For example, homework which is submitted one hour late is worth at most 90% of the total credit.
In unusual circumstances, such as extreme illness or injury (documented by a doctor's note), family emergencies, etc., please contact the instructor as early as possible to arrange accomidations.
I am happy to regrade any assignmentss or exam problems which you think were unfair or incorrect. Please bring me the original assignment, plus a written explanation of your question or complaint, within two weeks of the time the paper in question is graded and returned to you.
In the context of this course, I encourage students to discuss general course material, which includes studying for exams, sharing notes if a student must miss class, and working on any practice problems which are assigned. You are also allowed to turn in homework assignments in pairs. I also encourage you to discuss problems with other students, but please be careful to write up all solutions separately and do not copy any material from another student. As a good rule of thumb, make sure to write your solutions without using any notes or papers written while talking to anyone other than your partner. Remember, you will be on your own in the exam, so it is in your own best interest to make sure that you really understand the material and can solve each problem on your own!
You are allowed to use outside sources of information in this class, including textbooks and webpages. If the complete and correct answer is on page 263 of the lecture notes, the best solution you can submit is "See page 263 of the lecture notes." Period. However, if you find a solution from any other source, such as a web page, a journal paper, a different algorithms textbook, or your mom, you must rewrite the solution in your own words, and you must properly cite your sources. Assume the grader has access to all the official course material, but nothing else. While we strongly encourge you to use any outside source at your disposal, please remember that the homework is supposed to demonstrate that you understand of the material, not just how to use Google. (In particular, if you blindly copy an incorrect solution, don't expect to get very many points for it!)
Students who violate academic integrity policies will be reported to the department, particularly in cases where relevant sources are not cited or in cases of direct copying of another student's work. First time offenses on homework will result in a minimum of a failing grade on the assignment in question, with egregious or repeated offenses resulting in failure in the course. In addition, students may be referred to the College of Arts and Sciences for further disciplinary action.
A statement of minimum standards for student academic integrity at Saint Louis University is described here; I expect full compliance with the policies described.