Special-topic Lecture Bioinformatics: Processing of Biological Data

Tutors:

Markus Hollander, Andreas Denger, Nicolas Künzel, Trang Do Hoang Thu

Lecture:

Tuesday, 10:15 am - 11:45 am -> video lecture

First lecture: May 5th, 2020;

Students intending to take this course should send an
e-mail to kerstin.gronow-p@bioinformatik.uni-saarland.de
so that they can be registered as participants in
Microsoft Teams in the course named "PBD-SS2020".

Tutorial:

new date: Wednesday, 12:00 pm - 2:00 pm -> video tutorial

Video Lectures

The video lectures take place on Microsoft Teams in the course named "PBD-SS2020".

The username is <your student ID>@uni-saarland.de (e.g. s9example@uni-saarland.de) and the password is the same one you use for the LSF/HISPOS or other university logins.

More information on how to use Microsoft Teams at Saarland University can be found here.

Exam:

Oral exams will take place at CBI, room 1.06 from July 27th to July 31st, 2020.
Students not physically present in Saarland can take an online exam instead. Please regard the registration deadline of July 24th, 2020, for this exam at LSF. A later registration will not be possible.

Information:

This course can be used as a "Spezialvorlesung der Bioinformatik/Special-topic Lecture Bioinformatics"

Requirements:

Intermediate programming skills in Python

Content:

    • clustering of data
    • principal component analysis
    • differential expression analysis
    • removal and correction of data outliers; prediction of missing values
    • processing of proteomics data; imputation of missing values
    • peak assignment
    • shape detection
    • functional annotation
    • protein structure data (Protein DataBank); thermal mobility; titration states; hydration sites; PDBcheck
    • molecular dynamics simulations; time correlation of snapshots
    • multi-variate analysis
    • analysis of multi-dimensional data; data integration

Conditions for certification:

Students need to pass the final exam.

There will be about six bi-weekly graded assignments and tutorial sessions. Students need to get at least 50% of the points from the assignments to be admitted to the final exam. 

Schein/Certification:

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

Leistungspunkte/Credits:

5 (2 V + 1 Ü)

Language

This course is taught in English language.

Lectures:

Students intending to take this course should send an e-mail to kerstin.gronow-p@bioinformatik.uni-saarland.de so that they can be registered as participants in Microsoft Teams in the course named "PBD-SS2020"

Lecture 1, May 5 pdf ppt1-audio
ppt2-audio
ppt3-audio
ppt4-audio
Lecture 2, May 12 pdf ppt1-audio
ppt2-audio
ppt3-audio
Assignment 1
Supplement 1
Lecture 3, May 19 pdf ppt1-audio
ppt2-audio
ppt3-audio
Lecture 4, May 26 pdf ppt1-audio
ppt2-audio
ppt3-audio
Assignment 2
Supplement 2
Lecture 5, June 2 pdf
Lecture 6, June 9

[Swapped with lecture 7!]

pdf ppt1-audio

ppt2-audio

ppt3-audio

ppt4-audio

Assignment 3
Supplement 3
Lecture 7, June 16 pdf
Lecture 8, June 23 pdf Assignment 4

Supplement 4

Assignment 4 - Solution

Lecture 9, June 30 pdf
Lecture 10, July 7 pdf Assignment 5

Supplement 5

Lecture 11, July 14 pdf