Universität Wien

300191 UE Bioinformatics for non-bioinformaticians - how to build and analyse a transcriptome (2020W)

3.00 ECTS (3.00 SWS), SPL 30 - Biologie
Continuous assessment of course work
Moodle

Registration/Deregistration

Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).

Details

max. 16 participants
Language: English

Lecturers

Classes (iCal) - next class is marked with N

The course will run from 9am until 1pm Monday - Friday from the 01/02/2020 until the 12/02/2020.

There will be an online pre-meeting on the 5.10, at 14:00h. Attendance is mendatory to be able to take the course. We will send instructions via e-mail a few days before.

  • Monday 01.02. 09:00 - 13:00 Übungsraum 2
  • Tuesday 02.02. 09:00 - 13:00 Übungsraum 2
  • Wednesday 03.02. 09:00 - 13:00 Übungsraum 2
  • Thursday 04.02. 09:00 - 13:00 Übungsraum 2
  • Friday 05.02. 09:00 - 13:00 Übungsraum 2
  • Monday 08.02. 09:00 - 13:00 Hörsaal 1, UZA 1, Biozentrum Althanstraße 14, 1.008A EG
  • Tuesday 09.02. 09:00 - 13:00 Übungsraum 4
  • Wednesday 10.02. 09:00 - 13:00 Übungsraum 4
  • Thursday 11.02. 09:00 - 13:00 Übungsraum 4
  • Friday 12.02. 09:00 - 13:00 Übungsraum 4

Information

Aims, contents and method of the course

This course is aimed at masters students who have little or no experience with bioinformatics but are interested in learning the basics of transcriptomics. Students will be introduced to:
1) the Linux operating system and the command line
2) Next Generation Sequencing (NGS) data quality control and transcriptome assembly
3) Gene annotation using tools such BLAST, HMMER, signalP, TMHMM etc.
4) Data mining
5) Phylogenetics

Students will be introduced to the command line and will learn through the practical application of various freely available bioinformatic software packages. In the first week, each student will build their own transcriptome from publicly available data and this will be used in the second week to learn about the basics of gene annotation and phylogeny.

Students are required to bring their own laptop.

We will try to teach this course in person to provide the best learning environment, but depending on the Covid situation we may have to adapt to other methods. Students will be informed about any changes.

Assessment and permitted materials

Assessment will involve:
1) a multiple choice exam at the end of the first week - 30 % of total grade
2) the submission of a data sheet detailing the results of their transcriptome assembly and analysis 30%
3) a short group presentation comparing the results of the group members - 40%

Minimum requirements and assessment criteria

1- Basic English skills;
2- Basic knowledge on molecular biology: DNA replication, transcription, translation.

Examination topics

Lectures and practical work.

Reading list

1. Christoph Bleidorn - Phylogenomics An Introduction (Book)
2. Molecular Biology of the cell (Book)

Association in the course directory

MZO W-3, MES5, MGE III-2, M-WZB

Last modified: Th 23.02.2023 00:25