Bioinformatics 3

Overview

Tutors

Markus Hollander, Trang Do, Hanah Betsy Robertson, Sudharshini Thangamurugan, Aram Papazian

Semester
SS 2024
Type
Lecture
Language
English
Credit Points
9 CP
Lecture

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

Tutorial

to be announced,
Microsoft Teams

Exam

to be announced

Re-Exam

to be announced

Registration

For organizational reasons (add to MS Teams group), 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, April 16
Lecture 2
Thu, April 18
Lecture 3
Tue, April 23
Lecture 4
Thu, April 25
Lecture 5
Tue, April 30
Lecture 6
Thu, May 2
Lecture 7
Tue, May 7
Lecture 8
Tue, May 14
Lecture 9
Thu, May 16
Lecture 10
Tue, May 21
Lecture 11
Thu, May 23
Lecture 12
Tue, May 28
Lecture 13
Tue, June 4
Lecture 14
Thu, June 6
Lecture 15
Tue, June 11
Lecture 16
Thu, June 13
Lecture 17
Tue, June 18
Lecture 18
Thu, June 20
Lecture 19
Tue, June 25
Lecture 20
Thu, June 27
Lecture 21
Tue, July 2
Lecture 22
Thu, July 4
Lecture 23
Tue, July 9
Lecture 24
Thu, July 11
Lecture 25
Tue, July 16
Lecture 26
Thu, July 18
Lecture 27
Tue, July 23
Lecture 28
Thu, July 25

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, April 18
Due
Tue, April 30

10:00 am

Assignment 2
Tutor
Markus Hollander
Start
Tue, April 30
Due
Tue, May 7

10:00 am

Assignment 3
Tutor
Markus Hollander
Start
Tue, May 7
Due
Tue, May 14

10:00 am

Assignment 4
Tutor
Aram Papazian
Start
Tue, May 14
Due
Tue, May 21

10:00 am

Assignment 5
Tutor
Aram Papazian
Start
Tue, May 21
Due
Tue, May 28

10:00 am

Assignment 6
Tutor
Trang Do
Start
Tue, May 28
Due
Tue, June 4

10:00 am

Assignment 7
Tutor
Hanah Betsy Robertson
Start
Tue, June 4
Due
Tue, June 11

10:00 am

Assignment 8
Tutor
Hanah Betsy Robertson
Start
Tue, June 11
Due
Tue, June 18

10:00 am

Assignment 9
Tutor
Sudharshini Thangamurugan
Start
Tue, June 18
Due
Tue, June 25

10:00 am

Assignment 10
Tutor
Sudharshini Thangamurugan
Start
Tue, June 25
Due
Tue, July 2

10:00 am

Tutorials

Tutorials take place online in Microsoft Teams after the submission of their corresponding assignment. The currently proposed time slot is Tuesdays from 1:00 pm to 2:00 pm. However, a survey will be conducted at the beginning of the lecture to account for possible collisions with other lectures and tutorials.

Tutorial 1
to be announced
Tutorial 2
to be announced
Tutorial 3
to be announced
Tutorial 4
to be announced
Tutorial 5
to be announced
Tutorial 6
to be announced
Tutorial 7
to be announced
Tutorial 8
to be announced
Tutorial 9
to be announced
Tutorial 10
to be announced