Bioinformatics

Module code

mlsBioInfo-01a

Abbreviated title

BioInfo

Module components

Lecture, seminar, tutorial

When

Semester 2

Module coordinator/

Organiser

D. Ellinghaus

IKMB

Lecturers

D. Ellinghaus (IKMB) and assistants

Contact hours

Lecture 2 CH           Seminar 1 CH           Tutorial 2 CH

Workload

Total: 150 h

Lecture: 60 h
Attendance time 26 h, preparation 14 h, revision 20 h
Seminar: 30 h
Attendance time 14 h, preparation 14 h, revision 2 h
Tutorial: 60 h
Attendance time 26 h, revision 34 h

Credit points

5 (lecture 2 CP, seminar 1 CP, tutorial 2 CP)

Requirements

-

Expected outcome

Knowledge: Students

- are familiar with the basics and common terminology of bioinformatics (developing solutions for collecting, managing and interpreting biological data)

- can name the most important software applications and resources and describe them exemplarily.

Skills: Students

- can explain how algorithms discussed in the lecture work (e.g. BLAST)

- can elucidate how a short R-script functions

- can apply analytical tools.

Competences: Students

- can select and apply suitable software for a specific bioinformatics problem

- can interpret results the analytical tools used in the tutorial deliver.

Content

Lecture: Overview of bioinformatical work areas; phylogenetic relationships; sequence alignment (e.g. BLAST); gene prediction, genome assembly, protein structure prediction, pathway reconstruction (protein-protein interactions), genetic algorithms (linkage/association).

Tutorial: LINUX command line (e.g. processing of large text files); introduction to R, different browsers (NCBI, ENSEMBL, UCSC); data bases and queries; sequence alignment, protein structure prediction; in silico evaluation of mutations; developing phylogenetic family trees with sequencing data, analysing gene expression data, eQTL analysis, linkage study analysis, GWAS.

Seminar:

Consolidation of knowledge by discussing current scientific publications.

Module evaluation/

exam

Graded

Written exam

Media used

PPT presentations, scripts

Literature

Alterovitz G, Ramoni M (ed.), Knowledge-based bioinformatics: From analysis to interpretation (John Wiley & Sons 2010)

Current scientific publications