Examination slots July 4th
| Baukmann | canceled |
| Beslic | 09:30 |
| blocked | |
| blocked | |
| blocked | |
| Korzec | 11:30 |
| Mengüllüoglu | 12:00 |
| Sliwa | 12:30 |
| canceled | |
| Tiwari | 16:00 |
| Toorn | 16:30 |
| Krause | 17:00 |
Examination slots July 5th
| Dawid | 11:30 |
| Sullivan | 12:00 |
| Kaptan | 12:30 |
Information for students
This is an elective course (Wahlpflichtveranstaltung) for students in the MSc Bioinformatics.
The modul 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: We will start with an intro into compact data structures and vectorized computing. Then we will deal with methods for approximate searching and variant detection in sequences, the construction and use of modern index structures and methods for RNA sequence analysis and variant detection.
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.
Seminar group A: Baukmann, Beslic, Dawid, Habibolahi
Seminar group B: Kaplan, Korzec, Kranz, Krause
Seminar group C: Mengüllüoglu, Ravishankar, Shell, Sheshadri
Seminar group D: Sliwa, Sullivan,Tiwar, Toom
Content
| Date | Event | |
|---|---|---|
| 09.4. | L: Compact data structures: Entropy and Coding | |
| 12.4. | L: Compact data structures: Arrays | |
| 16.4. | L: Compact data structures: Bitvectors with rank and select I | |
| 18.4. | L: Compact data structures: Bitvectors with rank and select II | |
| 23.4. | Exercise | |
| 25.4. | Exercise | |
| 26.4. | S: Fast, Small, Simple Rank/Select on Bitmaps (A) | |
| 30.4. | L: Vectorization | |
| 02.5. | Exercise | |
| 03.5. | S: Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading (B) | |
| 07.5. | Review 1 | |
| 09.5. | L: Suffix array construction in linear time | |
| 10.5 | L: LCP computation in linear time | |
| 14.5 | Exercise | |
| 16.5. | S: DisLex: a transformation for discontiguous suffix array construction (C) | |
| 17.5. | Review 2 | |
| 21.5. | L: Onedirectional FM-indices | |
| 23.5. | L: Bidirectional FM-indices | |
| 24.5. | Exercise | |
| 28.5. | Exercise | |
| 31.5. | S: FMtree: A fast locating algorithm of FM-indexes for genomic data (D) | |
| 04.6. | Review 3 | |
| 06.6. | L: Filter algorithms I: PH-based, counting based | |
| 07.6. | L: Filter algorithms II: 01*0-Filters | |
| 11.6. | Exercise | |
| 13.6. | Exercise | |
| 14.6. | S: Optimum Search Schemes (A+B) | |
| 18.6 | L: Filter algorithms III: Search schemes | |
| 20.6. | L: Filter algorithms IV: Bloom filter variations | |
| 21.6. | Exercise | |
| 25.6. | S: 01*0 Seeds (C) | |
| 27.6. | S: Mantis (D) | |
| 28.6. | Review 4 | |
| 02.7. | L: RNA analysis | |
| 04.7. | Oral examinations |