Advanced Algorithms in Bioinformatics S21
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Description

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:

  • Paradigmen für approximative, semiglobale Alignments (read mapping)
  • Methoden zur Genomassemblierung und Metagenomassemblierung
  • Methoden zum Bestimmen genetischer Variationen (SNVs, SNPs, CNVs)
  • Algorithmische Probleme bei der Quantifizierung mit Hilfe von NGS Daten

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":

  • You have to be prepared to give a seminar talk (if it's your group's turn). This will be also done via a webex video meeting until further notice.
  • In addition you need to reach 50% of all points of the reviews. This will be done online.

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
Basic Course Info

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

Study Regulation

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

Advanced Algorithms in Bioinformatics S21
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Main Events

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

Accompanying Events

Day Time Location Details
Thursday 14-16 Online Übung 01

Advanced Algorithms in Bioinformatics S21
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