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: