Algoritmi e Linguaggi per Bioinformatica: Algoritmi

Attention!     This is the webpage of the course given in the 2nd term of 2011/2012.
The new course (2nd term 2012/13) may have a different webpage.

Title of course: Algoritmi e Linguaggi per Bioinformatica: Algoritmi (2nd term of 2011/2012)
Lecturer:Zsuzsanna Lipták
email: zsuzsanna DOT liptak AT univr DOT it  
(Please put "Corso Algoritmi di Bioinformatica" in the subject line.)
Times: Tue 1.30 - 4.30 and Wed 8.30 - 10.30
Place:Lecture hall H
Hours (2011/12):
Tue 4.30 - 5.30 and Wed 10.30 - 11.30 (after the lectures)
and by appointment
Office:Ca' Vignal, 2, 1st floor, right corridor, stanza 1.79

News:     Appello 8 e 25 febb 2012:

Detailed information on the course in the spring term 2011/12 (schedule, materials) can be found here. (Ignore the part about the projects!)
Here is a list of things you should know for the exam.

Information on past exams can be found here.

Current information: schedule, materials.

Note to students: If you have not yet received an email from me but you are following this course (and want to get the credits) then please send me an email, so I can include you in the mailing list.

Goals of the course: 1. to learn about some basic problems and algorithms behind common bioinformatics applications (alignment, sequence similarity, phylogenetics), and 2. to get an idea of some basic computational problems (complexity, efficiency, limitations).

Credits: The credits for this course are given together with the first part of this module (Linguaggi, 1st term 2011/2012). The total grade (voto) for the module "Algoritmi e Linguaggi per Bionformatica" will be 50% Linguaggi and 50% Algoritmi. The grade (voto) for this course (Algoritmi) is given in the following way: 50% written exam, 50% project. The written exam consists of 2 parts: one midterm (which covers the first half of the course) and one final (which covers the second half). Alternatively, one can take only one final exam (which covers the whole course). The project can be done in groups of 1 to 3, and will be chosen together according to the students' backgrounds and interests.

Language: Lectures are in English; however, questions can be asked in English or Italian. Exams will be in Italian only (but answers can be given in English if you choose).

A note on attendance: As in most university courses, attendance of classes is not mandatory. All of what I teach in this course is completely standard and is contained in any algorithmically oriented bioinformatics book (see list on this page). In the exam, you will be asked to do things like compute an alignment of two strings, given a score function. You can learn this from any book or online course. However, I strongly believe that one gains much more from attending a course than from only studying by oneself. University classes give the student the opportunity of following a live course given by a live lecturer. If nothing else, attending the course forces you to spend a certain amount of time each week studying for this course. No handouts or slide presentations can completely substitute a lecturer. So if you can in any way make it, I would advise you to attend. If you can't, you have to rely on the notes of your colleagues and/or on books.

Tentantive schedule (updated):
(For the real one, please check here)

Books: There are many books on bioinformatics, and most, if not all, will contain what we cover in this course. The following is a selection of my own.