Information for students
Exam slots:
The exam will be in my office, T9 room 012.
Time slot |
Last name |
First name |
| 21.7. : 8:30 | Lutfi | Ahmad |
| 21.7. : 9:00 | Willemsen | Myrthe |
| 21.7. : 9:30 | Okroznik | Nina |
| 21.7. : 10:00 | Lopez Ruiz de Vargas | Sara |
| 21.7. : 10:30 | Petrov | Tino Marvin |
| 21.7. : 11:00 | Pipart | Julian |
| 21.7. : 11:30 | Schmitz | Dominik |
| 26.7. : 13:00 | Droop | Felix |
| 26.7. : 13:30 | Glöckner | Sina |
| 26.7. : 14:00 | ||
| 26.7. : 14:30 | Waschischeck | Tom |
| 26.7. : 15:00 | Battur | Namuun |
| 27.7. : 14:30 | Muck | Aleksandr |
| 27.7. : 15:00 | Scheil | Patricia |
| 27.7. : 15:30 | Shyamsaisundar | Vishnushiri |
| 27.7. : 16:00 | Brenningmeyer | Jule Marie |
This is a mandatory course for students in the MSc Bioinformatics.
The module consists of a lecture, a seminar and exercises which will be blocked according to the respective topic. This means we will have first several lectures, followed by exercises, followed by seminars. One block is concluded with a review test about the content.
Content: Requirements for "aktive Teilnahme":
- You have to be prepared to give a seminar talk (if it's your group's turn).
- In addition, you need to reach 50% of all points of the reviews.
Contact:
- knut.reinert@fu-berlin.de
- svenja.mehringer@fu-berlin.de
- s.gottlieb@fu-berlin.de (If you have any question, write me!, or come to T9/R010)
Content
There are corresponding lecture videos from this year (2022) and previous year (2020).
| # | Date | Event |
|---|---|---|
| 1 | 21.04. | L: Suffix array search |
| 2 | 26.04 | L: LCP computation |
| 3 | 26.04. | L: Suffix array construction |
| 4 | 28.04. | Exercise |
| 5 | 03.05. | Exercise |
| 6 | 03.05. | Exercise |
| 7 | 05.05. | S: DisLex: a transformation for discontiguous suffix array construction (A) |
| 8 | 10.05. | Review 1 |
| 9 | 10.05. | L: Onedirectional FM-indices (Lehrprobe Thilo Muth) |
| 10 | 12.05. | Exercise |
| 11 | 17.05. | L: Bidirectional FM-indices |
| 12 | 17.05. | L: Extensions of FM-indices |
| 13 | 19.05. | Exercise |
| 14 | 24.05. | Exercise |
| 15 | 24.05 | S: Chapters 11.1 and 11.2 of the book Compact Data structures (B) |
| 16 | 31.05 | Review 2 |
| 17 | 31.05. | L: k-mer based analysis I |
| 18 | 02.06. | L: k-mer based analysis II |
| 19 | 07.06. | L: k-mer based analysis III |
| 20 | 07.06. | Exercise |
| 21 | 09.06. | Exercise |
| 22 | 14.06. | S: Quotient filter (C) |
| 23 | 14.06. | S: Counting Quotient filter (D) |
| 24 | 16.06. | Review 3 |
| 25 | 21.06. | L: Filter I |
| 26 | 21.06. | L: Filter II |
| 27 | 23.06. | Exercise |
| 28 | 28.06. | Exercise |
| 29 | 28.06. | S: Genmap (E) |
| 30 | 30.06 | S: Adaptive Seeds (F) |
| 31 | 05.07. | Review 4 |
| 32 | 05.07. | L: Haplotyping I |
| 33 | 07.07. | L: Haplotyping II |
| 34 | 12.07. | Exercise |
| 35 | 12.07. | Exercise |
| 36 | 14.07. | S: HapCUT: an efficient and accurate algorithm for the haplotype assembly problem (To be determined) |
| 37 | 19.07. | Q&A |
| 38 | 19.07. | Buffer |
| 39 | 21.07. | Exams |
Seminar Groups
| Glöckner, Sina | Seminar Group A |
| Okroznik, Nina | Seminar Group A |
| Willemsen, Myrthe | Seminar Group A |
| Battur, Namuun | Seminar Group B |
| Shyamsaisundar, Vishnushiri | Seminar Group B |
| Thothathri, Gokul | Seminar Group B |
| Petrov, Tino | Seminar Group C |
| Lutfi, Ahmad | Seminar Group C |
| Pipart, Julian | Seminar Group C |
| Brenningmeyer, Jule Marie | Seminar Group D |
| Scheil, Patricia | Seminar Group D |
| Schmitz, Dominik | Seminar Group E |
| Waschischeck, Tom | Seminar Group E |
| Wohlfarth, Friederike | Seminar Group E |
| Lopez Ruiz de Vargas, Sara | Seminar Group F |
| Muck, Aleksander | Seminar Group F |
| Droop, Felix | Seminar Group F |