1MB304: Discrete structures for bioinformatics II 2008 


The course teaches computational methods for some of the core applications
of bioinformatics:


After this course students should be able to: 1.describe the different algorithm design techniques and discuss their pros and cons.
2.sketch a solution to a bioinformatics problem using pseudocode and analyze its time/space complexity
3.recognize the algorithm design technique used in an existing bioinformatics solution, analyze its time/space complexity and the plausibility of using other techniques.
4.translate a given a biological problem into a representation that lends itself to be solved by one of the techniques, and discuss/argue for your solution.

When/where? 
Topics 
Material 

2008.09.05 Friday 1012 Lärosal 1, EBC 

Lecture 1 Chapter 2 
WEEK 36  
2008.09.05 Friday 1315 Lärosal 1, EBC 

Lecture 2 Chapter 4 

2008.09.09 Tuesday 1315 D1:411, BMC 
Exercise: Algorithms, complexity and exhaustive search  Exercise 1  WEEK 37  
2008.09.11 Thursday 1012 D1:411, BMC 

Lecture 3 Chapter 5 

2008.09.11 Thursday 1315 D1:411, BMC 

Lecture 4 

2008.09.12 Friday 1012 D1:411, BMC 
Exercise: Greedy algorithms  Exercise 2  
2008.09.16 Tuesday 10.0012.00 D5:206b, BMC 
Exercise: Dynamic programming  Exercise 3  WEEK 38  
2008.09.17 Wednesday Midnight 
Deadline: Exercise 1 (copy)  
2008.09.18 Thursday 1012 Lärosal 1, EBC 

Lecture 5 Chapter 11 

2008.09.19 Friday 1012 D1:419, BMC 
Exercise: Hidden Markov models  Exercise 4  
2008.09.19 Friday Midnight 
Deadline: Exercise 2 (copy)  
2008.09.23 Tuesday Midnight 
Deadline: Exercise 1 (corrected)
Deadline: Exercise 3 (copy) 
WEEK 39  
2008.09.26 Friday Midnight 
Deadline: Exercise 2 (corrected) Deadline: Exercise 4 (copy) 

2008.09.29 Monday 1315 D1:411, BMC 

Lecture 6 Chapter 11, 12.112.2 
WEEK 40  
2008.09.29 Monday 1517 PCrummet del A, BMC 
Exercise: Hidden Markov models (computer lab)  Exercise 5 Matlab HMM library 

2008.09.30 Tuesday 1315 D1:411, BMC 
Exercise: Mix of topics from the course  Exercise 6  
2008.09.30 Tuesday Midnight 
Deadline: Exercise 3 (corrected)  
2008.10.02 Thursday 1315 D1:411, BMC 

Lecture 7  
2008.10.03 Friday Midnight 
Deadline: Exercise 4 (corrected)  
2008.10.06 Monday Midnight 
Deadline: Exercise 5 (final, no student correction)  WEEK 41  
2008.10.07 Tuesday 1012 Chipset del B, BMC 
Computer project  Project description 

2008.10.07 Tuesday Midnight 
Deadline: Exercise 6 (copy)  
2008.10.08 Wednesday 1315 Chipset del B, BMC 
Computer project  
2008.10.09 Thursday 1012 Chipset del B, BMC 
Computer project  
2008.10.13 Monday 1012 Chipset del B, BMC 
Computer project  WEEK 42  
2008.10.14 Tuesday 1315 Chipset del B, BMC 
Computer project Course evaluation! 

2008.10.14 Tuesday Midnight 
Deadline: Exercise 6 (corrected)  
2008.10.17 Friday 12.00 (Midday) 
Deadline: Project report  
2008.10.20 Monday 1315 D1:415, BMC 

WEEK 43  
2008.10.23 Thursday 914 B10:1, BMC 
Exam  Relevant previous exams: 2006 (solutions) 2007 (solutions) 