Pattern Recognition in Bioinformatics Q3/2012
Announcements
- 28/02/12: Preliminary exam questions available.
- 23/02/12: The description of mandatory project 3 (due Mon Mar 12) is available.
- 08/02/12: Today at the lecture we decided that the oral exam will be on Tuesday, March 20.
- 07/02/12: The description of mandatory project 2 (due Wed Feb 22) is available.
- 27/01/12: The description of mandatory project 1 (due Wed Feb 8) is available.
- 07/12/11: Initial www-page ready.
About
Bioinformatics is about developing and applying algorithms for analysis of biological data. The amount of sequence data is growing fast, and many interesting problems are based on the analysis of large sets of sequence data. This class covers concrete algorithms for pattern recognition and discovery in sequence data based on hidden Markov models (HMMs) and stochastic context-free grammars (SCFGs), and examples of their application on biological sequences.
The participants will after the course have insight into algorithms for pattern recognition in biological sequences (DNA, RNA, and protein) and practical experience with implementation of these algorithms. The working method of the course will also train the participants to plan and complete projects and to communicate professional issues.
The participants must at the end of the course be able to:
- define and describe basic problems in pattern recognition in biological sequences.
- apply and explain known techniques for design of algorithm for pattern recognition in biological sequences.
- implement and evaluate concrete algorithms based on known techniques for pattern recognition in biological sequenc
Schedule
Lectures take place:
- Monday 10.15-12.00 in DI-Nygaard 184.
- Wednesday 15.15-16.00 in DI-Nygaard 184.
First lecture is on Monday, January 23.
Literature
We will use research papers and excerpts from text books which will be handed out in class or made available for download.
Exam and Projects
The final exam is an individual oral exam (20 min) which includes a presentation based on an exam question followed by a general discussion of related topics and mandatory projects. You should prepare a 10-12 minutes presentation for each exam question (you can bring your notes to the exam).
The exam curriculum is every reference listed under "Reading material" on the weekly schedule for Week 1-7, and the descriptions of the mandatory projects. The exam date is Tuesday, March 20, 2012. The exam will take place in 1111-100 at BiRC. To participate in the final oral exam each student must complete all mandatory projects.
Lecturer
If you have any comments or questions related to the course, do not hesitate to contact one of the lectures:
Office: 1110.326
E-mail: mailund [at] birc.au.dk
Christian Nørgaard Storm Pedersen
Office: 1110.325
E-mail: cstorm [at] birc.au.dk