Ziele:
Die Studentinnen und Studenten erlangen ein tieferes Verständnis für grundlegende algorithmische Konzepte im Bereich der Analyse genomischer Sequenzen vor dem Hintergrund aktueller Forschungsrichtungen der Bioinformatik und Biotechnologie. Sie verstehen verschiedene Paradigmen zur approximativen Suche, sie wissen, unter welchen Voraussetzungen bestimmte Algorithmen anderen vorzuziehen sind, und können wissenschaftliche Publikationen auf dem Gebiet entsprechend einschätzen.
Es werden vertieft Themen aus beispielsweise folgenden Gebieten behandelt:
Alle weiteren Informationen im Whiteboard: https://mycampus.imp.fu-berlin.de/portal
Webex room:
Webex-room for seminar: https://rki.webex.com/meet/ng1
1 (Lecture+Seminar) https://fu-berlin.webex.com/meet/torsten.semmler
altternative room: https://rki.webex.com/meet/semmlert
Special Guest WebEX (Knut Reinert): https://fu-berlin.webex.com/meet/kreinert
2 (Exercises) https://fu-berlin.webex.com/meet/simon.gottlieb
Recorded Lectures:
https://box.fu-berlin.de/s/NFrsFZB3FZD7YMt
https://www.dropbox.com/sh/sqksd68450hopeu/AABMoote8hQU3S1zMkgpHmAHa?dl=0
Lectures K-mers (Knut Reinert) are HERE.
Contact:
semmlert@rki.de
simon.gottlieb@fu-berlin.de
eppingl@rki.de
wolfs@rki.de
Corona information:
1) Equipment
I assume you all have at least a smart phone. This can serve for sharing your screen when you write on a piece of paper, e.g. for the exercises.
If possible you could get something like a selfie tripod (look e.g. at Amazon).
Also, try out the FU WebEx application (https://portal.zedat.fu-berlin.de/services) on your laptop/smartphone/tablet.
2) there will be a Q&A session via webex. The date will be detemined...
3) Lecture
I will provide the lecture slides for each session. Please try to have a look at the lecture BEFORE the lecture session. On the date of the lecture I will open the WebEx room where you can join and share my screen with the lecture. You can then ask questions on the respective lecture parts.
4) Exercises will be similarly online
5) Reviews
We will write reviews at home. That means we will upload the review, you write it at your desk and submit the PDF or fotos of your results.
6) Seminars
Again, we will do it online. The seminar group will present the paper using prepared notes on paper (with smartphone see above) or tablet/laptop.
7) Once the restrictions are lifted, we continue normally at the university.
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":
Seminar group A: Max Bieniara, Nadja Mansurov
Seminar group B: Gracia Andriamiadana, Johanna von Wachsmann and Siddharth Annaldasula
Seminar group C: Swenja Wagner, Valentina Galeone and Lion Ward Al Raei
Seminar group D: Yiftach Kolb, Abhinav Mishra
Content:
# | Date | Event |
1 | 13.04. | Introduction |
2 | 15.04. | L: Suffix array search |
3 | 16.04. | L: LCP computation |
4 | 20.04. | L: Suffix array construction |
5 | 22.04. | Exercise |
6 | 23.04. | Exercise |
7 | 27.04. | S: DisLex: a transformation for discontiguous suffix array construction (A) |
8 | 29.04. | Review 1 |
9 | 30.04. | L: Onedirectional FM-indices |
10 | 04.05. | L: Compressing FM-indices |
11 | 06.05. | Exercise |
12 | 07.05. | Exercise |
13 | 11.05 | S: Chapters 11.1 and 11.2 of the book Compact Data structures (B) |
14 | 13.05 | ascension day |
15 | 14.05. | Review 2 |
16 | 18.05. | L: k-mer based analysis I |
17 | 20.05. | L: k-mer based analysis II |
18 | 21.05. | L: k-mer based analysis III |
19 | 25.05. | Exercise |
20 | 27.05. | Exercise |
21 | 28.05. | S: Quotient filter (C) |
22 | 01.06. | S: Counting Quotient filter (D) |
23 | 03.06. | Review 3 |
24 | 04.06. | L: Filter I |
25 | 08.06. | L: Filter II |
26 | 10.06. | Exercise |
27 | 11.06. | Exercise |
28 | 15.06 | S: Genmap (A) |
29 | 17.06. | S: Adaptive Seeds (B) |
30 | 18.06. | Review 4 |
31 | 22.06. | L: Haplotyping I |
32 | 24.06. | L: Haplotyping II |
33 | 25.06. | Exercise |
34 | 29.06. | S: (C+D) HapCUT: an efficient and accurate algorithm for the haplotype assembly problem |
35 | 01.07. | Buffer |
36 | 02.07. | Buffer |
37 | 06.07. | Q&A |
38 | 08.07. | Q&A |
39 | 13.07. | Exam |
Course No | Course Type | Hours |
---|---|---|
19405311 | Seminar | 2 |
19405301 | Vorlesung | 2 |
19405302 | Übung | 2 |
Time Span | 13.04.2021 - 13.07.2021 |
---|---|
Instructors |
Simon Gene Gottlieb
Knut Reinert
Torsten Semmler
Lennard Epping
Silver Anthony Wolf
|
0089c_MA120 | 2014, MSc Informatik (Mono), 120 LPs |
0262b_MA120 | 2012, MSc Bioinformatik (Mono), 120 LPs |
0262c_MA120 | 2019 (ÄO 2021), MA Bioninformatik (Mono), 120 LP |
Day | Time | Location | Details |
---|---|---|---|
Tuesday | 12-14 | A6/SR 032 Seminarraum | 2021-04-13 - 2021-07-13 |
Friday | 14-16 | A6/SR 032 Seminarraum | 2021-04-16 - 2021-07-16 |
Day | Time | Location | Details |
---|---|---|---|
Thursday | 14-16 | Online | Übung 01 |