Exam slots:
| Date/Time | Surname | First name | |
| 19.7.: 10:00 | Kmiecinski | Rene Wesley | |
| 20.7.: 9:30 | Shao | Zhiao | |
| 20.7: 11:00 | Musch | Vincent | |
| 20.7: 11:30 | Glöde | Svenja | |
| 20.7.: 13:30 | Zandvakili | Aboozar | |
| 20.7.: 14:00 | Bannwitz | Dominik | |
| 20.7.: 14:30 | Wild | Nora |
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":
Contact:
- knut.reinert@fu-berlin.de
- svenja.mehringer@fu-berlin.de
- s.gottlieb@fu-berlin.de (If you have any questions, write me!, or come to T9/R010)
Tuesdays: A3/SR 119
Thursdays: T9/055 Seminarraum
There are corresponding lecture videos from SS 2023 and SS 2022.
| # | Date | Event |
|---|---|---|
| 1 | 18.04. | L: Suffix array search |
| 2 | 18.04. | L: LCP computation |
| 3 | 20.04. | L: Suffix array construction |
| 4 | 25.04. | Exercise |
| 5 | 25.04. | Exercise |
| 6 | 27.04. | Exercise |
| 7 | 02.05. | S: DisLex: a transformation for discontiguous suffix array construction (G1) |
| 8 | 02.05. | Review 1 |
| 9 | 04.05. | L: Onedirectional FM-indices |
| 10 | 09.05. | L: Bidirectional FM-indices |
| 11 | 09.05. | L: Extensions of FM-indices |
| 12 | 11.05. | Exercise |
| 13 | 16.05. | Exercise |
| 14 | 16.05. | S: FM-trees (G2) |
| 15 | 18.05 | Holiday |
| 16 | 23.05 | Review 2 |
| 17 | 23.05. | L: k-mer based analysis I: Concentration bounds |
| 18 | 25.05. | L: k-mer based analysis II: Estimate cardinalities and minimizers |
| 19 | 30.05. | Exercise (2x) |
| 20 | 01.06. | Exercise |
| 21 | 06.06. | L: k-mer based analysis III: Storing sets of kmers |
| 22 | 06.06. | L: k-mer based analysis IV: Storing sets of sets of k-mers and sketching |
| 23 | 08.06. | L: k-mer based analysis V: Comparison of sets k-mers |
| 24 | 13.06. | Exercise |
| 25 | 13.06. | Exercise |
| 26 | 15.06. | S: Strobemers: Effective sequence similarity detection ... (G3) |
| 27 | 20.06. | Review 3 |
| 28 | 20.06. | L: Filter I |
| 29 | 22.06. | L: Filter II |
| 30 | 27.06 | L: Filter III |
| 31 | 27.06. | L: Filter IV: Verification: Myers Bitvector Algorithm |
| 32 | 29.06. | Exercise |
| 33 | 04.07. | Exercise |
| 34 | 04.07. | Exercise |
| 35 | 06.07. | S: Genmap (G4) |
| 36 | 11.07. | S: Adaptive Seeds (G?) |
| 37 | 11.07. | Review 4 |
| 38 | 13.07. | Q&A |
| 39 | 20.07. | Exams |
| Course No | Course Type | Hours |
|---|---|---|
| 19405311 | Seminar | 2 |
| 19405301 | Vorlesung | 2 |
| 19405302 | Übung | 2 |
| Time Span | 18.04.2023 - 18.07.2023 |
|---|---|
| Instructors |
Knut Reinert
|
| 0262c_MA120 | 2019 (ÄO 2021), MA Bioninformatik (Mono), 120 LP |
| Day | Time | Location | Details |
|---|---|---|---|
| Tuesday | 10-12 | A3/SR 119 | 2023-04-18 - 2023-07-18 |
| Thursday | 14-16 | T9/055 Seminarraum | 2023-04-20 - 2023-07-20 |
| Day | Time | Location | Details |
|---|---|---|---|
| ?? | ? - ? | Group 2 | |
| ?? | ? - ? | Group 5 | |
| ?? | ? - ? | Group 4 | |
| ?? | ? - ? | Group 1 | |
| ?? | ? - ? | Group 3 |
Hi all,
the next seminar on Tuesday will start at 9am.
Since all groups have already presented a paper, the last seminar will be a pure discussion. (Unless someone wants to present again?)
I expect all of you to read the paper and talk with me about it. This time I'll ask the questions and you try to answer (with me and the group). I expect everyone to at least say something once, so please read the paper so I don't have to think about what happens when I ask you something and you reply you haven't read it.
See you next week,
Svenja
Hi all,
the purpose of the seminar is to get you accustomed with current (sometimes less current) research areas, read and understand scientific publications and lead discussions.
In each seminar, one group will present the paper of interest and afterwards we will discuss it together.
What I expect from the presenting group:
The group should closely read the paper and present the major findings, algorithms, data structures or whatever is key to the publication. Make sure you try to work out "the main purpose of this paper (e.g. what does it make better, faster or what other advantage does it have for the scientific community). Having said that, I do not expect that you fully understand everything. I don't need you to become experts on the field, that would take too much time. I simply want you to dive into the topic. If you don't understand certain content (after researching it) you can present your issue and we can discuss this together with the group.
You can present slides (tell me in advance so I can organize a beamer) or just use the blackboard (preferred!). Ask yourself which lectures you can follow best, the ones that rush through slides or the ones that go through an example on the board with you. A mix is also fine.
As the presenting group, you will also lead the discussion. You will take questions and if there are none, you can ask the questions that you have. These are either things you did not understand yourself and we try to solve them in a group effort, or questions that open up a conversation like "What applications could this data structure have?".
What I expect from the non-presenting people:
I expect that each single person has at least briefly read the paper. If I ask "what's the main message of the paper", every person should be able to give an answer to that. It doesn't have to be correct nor complete but you should be able to say something in the right direction that can be picked up by others. Write down questions we can discuss in together. Also, please bring the paper with you, digital or as a print out. That way everyone can follow the discussion if we speak about certain paragraphs in detail.
In summary, I just want you to talk until everyone understood the paper.
See you soon,
Svenja
Hi all,
please sign up for a seminar group in the "Section Info" until 18.04.2023. Since not many have signed up for the course so far, we will make groups of 2 for now.
Everyone who has not signed up for a group until that date will be randomly assigned by me.
Best,
Svenja