Universität Wien

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

3.00 ECTS (3.00 SWS), SPL 30 - Biologie
Prüfungsimmanente Lehrveranstaltung
VOR-ORT
Moodle

An/Abmeldung

Hinweis: Ihr Anmeldezeitpunkt innerhalb der Frist hat keine Auswirkungen auf die Platzvergabe (kein "first come, first served").

Details

max. 16 Teilnehmer*innen
Sprache: Englisch

Lehrende

Termine (iCal) - nächster Termin ist mit N markiert

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.

  • Donnerstag 07.10. 11:30 - 12:30 Hörsaal 2, Biologie Djerassiplatz 1, 0.033, Ebene 0 (Vorbesprechung)
  • Montag 07.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Dienstag 08.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Mittwoch 09.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Donnerstag 10.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Freitag 11.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Montag 14.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Dienstag 15.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Mittwoch 16.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Donnerstag 17.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1
  • Freitag 18.02. 09:45 - 13:45 Seminarraum 1.8, Biologie Djerassiplatz 1, 1.007, Ebene 1

Information

Ziele, Inhalte und Methode der Lehrveranstaltung

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.

Art der Leistungskontrolle und erlaubte Hilfsmittel

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

Mindestanforderungen und Beurteilungsmaßstab

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;

Prüfungsstoff

Lectures and practical work.

Literatur

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

Zuordnung im Vorlesungsverzeichnis

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

Letzte Änderung: Di 24.01.2023 00:26