Algorithmic Bioinformatics

V+Ü Discrete Mathematics for Bioinformatics (P1)

Linear programming; Combinatorial optimization; Graph algorithms; Advanced data structures; Discrete modelling; RNA and protein structure analysis; Molecular evolution.

(19254)

Type

Vorlesung + Übung

Instructor

Knut Reinert, Prof. Dr. Alexander Bockmayr, Sandro Andreotti

Credit Points

4 + 4

Time

Lectures:
Tue
10-12
Takustr. 9
SR 006
 
Thu
10-12
Takustr. 9
SR 006
Exercises:
Mon
  12-14  
  Takustr. 9  
SR 046

 

Student Profile

MSc students of Bioinformatics: In the new "Studienordnung": Pflichtmodul P4.

HEADS UP: Since the update of the Content Management System can take up to several hours, we have installed a wiki where you can find additional information in a timely fashion. You can find it here.

Termine:

Begin lecture: 15.10.

Begin tutorials: week from 19.10.

Klausur: 11.02.2010  results

Nachklausur: results

Examination: tbd.

Review 1: 23.11.2009 - during tutorial

Review 2: 19.01.2010 - during lecture (results)

 

Slides & Scripts  

1. Linear_programming.pdf (AB)

2. Integer_Linear_programming.pdf (KR) (Example files for Soplex and vint and traf from the porta package)

3. LagrangianRelaxation.pdf (KR)

4. Amortized analysis (KR)

5. Hashing.pdf (KR)

6. Skiplists (KR)

7. ConstraintProgramming (AB) (Updated 15.12.)

8. Metaheuristics (AB)

9. GraphAlgorithms (AB)

10. Tree decomposition (KR)

11. Complexity (AB)

 

Exercises

Each week the students have to work through their assignments. It is not necessary to hand in the solutions. However, we strongly encourage to solve the problems for yourself. The week after the assignments the solutions are discussed in the exercises.

Exercises_1.pdf

Exercises_2.pdf (sol_4.pdf)

Exercises_3.pdf (gapped_trace.pdf)

Exercises_4.pdf

Exercises_5.pdf

Exercises_6.pdf

Exercises_7.pdf

Exercises_8.pdf

Exercises_9.pdf

Exercises_10.pdf

Exercises_11.pdf

Exercises_12.pdf

Exercises_13.pdf

 

Reviews

There will be two reviews to check whether you worked through the exercise assignments. Students have to pass those reviews in order to have their "aktive Teilnahme" confirmed!