Bioinformatics 3

Overview

Tutors

Markus Hollander, Trang Do Hoang Thu, Andreas Denger, Sudharshini Thangamurugan

Semester
WS 2022/23
Type
Lecture
Language
English
Credit Points
9 CP
Lecture

Tuesday and Thursday,
2:15 pm – 4:00 pm,
building E2.1 room 001

Tutorial

Monday,
2:15 pm – 3:45 pm,
Microsoft Teams

Exam
to be announced
Re-Exam
to be announced

Registration

For organizational reasons, if you want to participate, please register by email to Kerstin Gronow-Pudelek.

Requirements

Familiarity with contents of Bioinformatik I and II. The students will have to complete programming assignments e.g. with Python. This course can be taken as part of the Master program Bioinformatics.

Content

The course will cover methodological aspects of integrated biology and systems biology:

  • protein-protein interaction networks (mathematical graphs, Bayesian networks)
  • analysis of protein complexes (density fitting, Fourier transformation)
  • transcriptional regulatory networks (Boolean networks) including epigenetic modifications and micro RNAs
  • dynamic simulation of cellular processes (differential equation solvers, stochastic simulations)
  • metabolic networks (linear algebra)

Textbook

V. Helms, Principles of Computational Cell Biology, Wiley (2019)

Certification

Students need to pass the written final exam that will be scheduled near the end of the winter semester or the re-exam that will be scheduled at the beginning of the following summer semester.

Condition for participation in the final exam

At least half of the total points of the assignments has to be reached, which for 10 assignments means that students have to accumulate at least 500 points in total.

Lectures

Lectures take place on Tuesdays and Thursdays from 2:15 pm to 4:00 pm in building E2.1 room 001. The lecture slides are available in the Microsoft Teams group in the “General” channel under “Files”.

Lecture 1
Tue, October 25
Lecture 2
Thu, October 27
Lecture 3
Thu, November 3
Lecture 4
Tue, November 8
Lecture 5
Thu, November 10
Lecture 6
Tue, November 15
Lecture 7
Thu, November 17
Lecture 8
Tue, November 22
Lecture 9
Thu, November 24
Lecture 10
Tue, November 29
Lecture 11
Tue, December 6
Lecture 12
Thu, December 8
Lecture 13
Tue, December 13
Lecture 14
Thu, December 15
Lecture 15
Tue, December 20
Lecture 16
Thu, December 22
Lecture 17
Tue, January 3
Lecture 18
Thu, January 5
Lecture 19
Tue, January 10
Lecture 20
Thu, January 12
Lecture 21
Tue, January 17
Lecture 22
Thu, January 19
Lecture 23
Tue, January 24
Lecture 24
Thu, January 26
Lecture 25
Tue, January 31
Exam
to be announced
Re-Exam
to be announced

Assignments

Assignments will be uploaded to the Microsoft Teams group in the “General” channel under “Files” according to the schedule below. Our Assignment Guide contains more information about our assignment policies that should be read before beginning with an assignment.

Assignment 1
Tutor
Markus Hollander
Start
Thu, October 27
Due
Tue, November 8

10:00 am

Assignment 2
Tutor
Markus Hollander
Start
Tue, November 8
Due
Tue, November 15

10:00 am

Assignment 3
Tutor
Markus Hollander
Start
Tue, November 15
Due
Tue, November 22

10:00 am

Assignment 4
Tutor
Trang Do Hoang Thu
Start
Tue, November 22
Due
Tue, November 29

10:00 am

Assignment 5
Tutor
Trang Do Hoang Thu
Start
Tue, November 29
Due
Tue, December 6

10:00 am

Assignment 6
Tutor
Trang Do Hoang Thu
Start
Tue, December 6
Due
Tue, December 13

10:00 am

Assignment 7
Tutor
Andreas Denger
Start
Tue, December 13
Due
Tue, December 20

10:00 am

Assignment 8
Tutor
Andreas Denger
Start
Tue, December 20
Due
Tue, January 10

10:00 am

Assignment 9
Tutor
Sudharshini Thangamurugan
Start
Tue, January 10
Due
Tue, January 17

10:00 am

Assignment 10
Tutor
Sudharshini Thangamurugan
Start
Tue, January 17
Due
Tue, January 24

10:00 am

Tutorials

Tutorials take place online in Microsoft Teams from 2:15 to 3:45 pm, on Mondays a week after the due date of their corresponding assignment.

Tutorial 1
Markus Hollander
Mon, November 14

2:15 pm – 3:45 pm

Tutorial 2
Markus Hollander
Mon, November 21

2:15 pm – 3:45 pm

Tutorial 3
Markus Hollander
Mon, November 28

2:15 pm – 3:45 pm

Tutorial 4
Trang Do Hoang Thu
Mon, December 5

2:15 pm – 3:45 pm

Tutorial 5
Trang Do Hoang Thu
Mon, December 12

2:15 pm – 3:45 pm

Tutorial 6
Trang Do Hoang Thu
Mon, December 19

2:15 pm – 3:45 pm

Tutorial 7
Andreas Denger
Mon, January 9

2:15 pm – 3:45 pm

Tutorial 8
Andreas Denger
Mon, January 16

2:15 pm – 3:45 pm

Tutorial 9
Sudharshini Thangamurugan
Mon, January 23

2:15 pm – 3:45 pm

Tutorial 10
Sudharshini Thangamurugan
Mon, January 30

2:15 pm – 3:45 pm