Lecture: Algorithms in Bioinformatics II

 

Lecturer	Prof. Dr. Daniel Huson and Dr. Christoph Dieterich
Assistants	Christian Rausch  and Tobias Kloepper
Office hours	DH: Mondays 16-17h30, office C310a, Sand 14 CD: by appointment CR: Mondays 16-17h30, office C310a, Sand 14
Time	Monday 10:20-12 h, Wednesday 11:15-13 h
Place	A301, Sand 1
Tutorials	Mi: 16:00 - 17:30h Matthias Ziehm (matthias.ziehm_at_student.uni-tuebingen.de) and Do: 16:00 - 17:30h Robert Krug (robert.krug_at_gmx.net)
Time and Place
Credits	8 LP, 4+2 SWS
Turnus	yearly in WS
Modules	Diploma: Praktische Informatik; MSc Bioinformatik: Modul Bioinformatik I; MSc Informatik: Wahlfplichtmodul Praktische Informatik
Language	English

Description:

Core algorithmic problems in bioinformatics.

Schedule and script:

16.4.2007	12. HMMs (continued from last semester)
18.4.2007	13. Gene finding using HMMs
23.4.2007	14. Motif finding  *
25.4.2007	continued
30.4.2007	continued
2.5.2007	15. Suffix trees
7.5.2007	Suffix trees continued-Ukkonens algorithm
9.5.2007	Suffix trees continued-WOTD algorithm *
14.5.2007	Suffix trees continued-applications
16.4.2007	Suffix trees continued-more applications
21.5.2007	16. SVMs and kernel functions
23.5.2007	Mid-term exam
	Pfingsten
4.6.2007	17. DNA arrays *
6.6.2007	continued
11.6.2007	18. Genome assembly
13.6.2007	continued
18.6.2007	continued
20.6.2007	19. Phylogenetic networks
25.6.2007	continued
27.6.2007	20. New sequencing technologies and metagenomics
2.7.2007	21. Simulating sequencing *
4.7.2007	22. Metabolic networks  *
9.7.2007	continued
11.7.2007	23. Physical mapping
16.7.2007	Final exam (possible topics)
18.7.2007	continued

Oral exams for Diploma students: Topics marked * will not be part of the oral exam.

Assignments:

assign01.pdf   Supplementary data: assign01.zip
assign02.pdf   Supplementary data: assign02.zip
assign03.pdf   Supplementary data: assign03.zip
assign04.pdf   Supplementary data: assign04.zip
assign05.pdf   Supplementary data: assign05.zip
assign06.pdf
assign07.pdf   Supplementary data: assign07.zip
assign08.pdf   Supplementary data: assign08.zip
assign09.pdf   Supplementary data: assign09.zip
assign10.pdf
assign11.pdf
assign12.pdf

Requirements:

For Diplom students in their 6. semester or higher.
For Master students in their 2. semester.

Credits for this course:

Diploma students: To obtain a "Schein" for this course, you are required to regularly and actively participate in the problem sessions. Additionally, you must regularly hand in assignment sheets and obtain at least 60 % of all possible assignment points. Students are permitted to work in groups of up to two people per group.
Further, you must participate in both exams (mid-term and final) and, in each exam, obtain at least 30% of all points.

Master students: You must qualify for a "Schein" as described for Diploma students. Your final grade for this course
will be computed as the average grade obtained in the two exams.