300191 UE Bioinformatics for non-bioinformaticians - how to build and analyse a transcriptome (2021W)
Continuous assessment of course work
Labels
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).
- Registration is open from Th 09.09.2021 08:00 to Th 23.09.2021 18:00
- Deregistration possible until Su 31.10.2021 18:00
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
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
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
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;
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
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
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) PhylogeneticsStudents 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.