Universität Wien FIND
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300191 UE Bioinformatics for non-bioinformaticians - how to build and analyse a transcriptome (2021W)

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

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

Vorbesprechung:
Date: 07.10.21
Time: 11:30 until 12:30
Hörsaal 2 / Stock: EG00 - Nr.: 0.033
1030 Wien, Djerassiplatz 1

The course is scheduled to start in the second week of February 2022 (end of the winter semester) from 07.02 until 18.02 (09:45 - 13:45). However, due the Covid situation changes can occur.

Thursday 07.10. 11:30 - 12:30 Hörsaal 2, Biologie Djerassiplatz 1, 0.033, Ebene 0 (Kickoff Class)
Monday 07.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Tuesday 08.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Wednesday 09.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Thursday 10.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Friday 11.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Monday 14.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Tuesday 15.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Wednesday 16.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Thursday 17.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
Friday 18.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1

Information

Aims, contents and method of the course

This course is aimed at Master/PhD 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 command line application
2) Next Generation Sequencing (NGS) data quality control and transcriptome assembly (Illumina)
3) Gene annotation using tools such BLAST, HMMER, signalP, TMHMM etc.
4) Data mining
5) Gene expression quantification
6) Phylogenetics

Students will be introduced to the command line and will "learn by doing" many practical exercises related to a typical "transcriptome project" workflow. Each student with the aid of the teachers will check the quality of pre-selected transcriptomes, assemble them, and will be introduced through a series of theoretical and practical lectures/exercises to the basics of gene annotation, quantification, and phylogeny.

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.

*Students are required to bring their own laptop.

*In the previous years (2016-2020) we had a massive number of preregistered students (>50) for the 16 spots we offer. We recommend the allocation of the maximum number of points one can to increase the chances of participate in next version of this course.

Assessment and permitted materials

Assessment will involve:
1) a multiple choice exam at the beginning of the second week - 30 % of total grade
2) the submission of a data sheet (bioinformatics protocol) in the last day of the course detailing the command line used and the results of the transcriptome analyses - 30 % of total grade
3) a short group presentation comparing the results of the group members - 40% of the total grade

Minimum requirements and assessment criteria

1- Advanced oral and writing English skills;
2- Basic knowledge on molecular biology: DNA replication, transcription, translation.
3- Eager to learn the wonders of bioinformatics;

Examination topics

Lectures and practical work.

Reading list

1. Christoph Bleidorn - Phylogenomics An Introduction (Book)
2. Molecular Biology of the cell (Book)
3. Diverse scientific papers provided by the teachers

Association in the course directory

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

Last modified: Tu 24.01.2023 00:26