Welcome to DataScience in Bioinformatics in the WS 2023/24!
We will start on the 16.10.2023 at 10 am with an introductory meeting. Afterwards we will provide you with some basic information about viruses and bacteria. Then we will familiarize ourselves with various bioinformatic toolboxes that are used to analyze sequencing results. We will then use these toolboxes to create a small pipeline that will allow automated analysis of sequences. You will learn about the methods used for this kind of analysis like filtering, assembly and variant calling. Coding will be done in python (python pre-skills required) and the pipeline will be created with snakemake, a popular workflow management system.
So far the module is planned as virtual only and a meeting takes place every monday at 2 pm starting at the 23.10.2023 and ends with a meeting on the 29.01.2024. The final code for the project needs to be handed in at latest on Monday, 19.02.2024. The final presentations will be on the 04.03.2024.
| Day | Date | Topics | Lecturers |
|---|---|---|---|
| 1 | 16.10.2023 | Introduction, Questions, Presentation Topics | Folker Meyer |
| 2 | 23.10.2023 | Biology basics, Viruses | Ivana Kraiselburd |
| 3 | 30.10.2023 | Conda, Bioinformatic Basics, Git, Reproducibility | Folker Meyer |
| 4 | 06.11.2023 | Snakemake | Johannes Köster |
| 5 | 13.11.2023 | Sequence Processing Presentations | Adrian Doerr, Simon Magin |
| 6 | 20.11.2023 | Genome Reconstruction Presentations | Josefa Welling, Ann-Kathrin Brüggemann |
| 7 | 27.11.2023 | Genome Analysis Presentations | Ivana Kraiselburd, Folker Meyer |
| 8 | 04.12.2023 | Lineage Assignment Presentations | Alexander Thomas, Josefa Welling |
| 9 | 11.12.2023 | Q&A - Help session | all |
| 10 | 18.12.2023 | Q&A - Help session | all |
| 11 | 08.01.2024 | Q&A - Help session | cancelled |
| 12 | 15.01.2024 | Q&A - Help session | all |
| 13 | 22.01.2024 | Q&A - Help session | all |
| 14 | 29.01.2024 | Q&A - Help session | all |
Here you can find the presentation topics and when and by whom they will be presented. Students are shown with their intials, e.g. Prof. Folker Meyer would be FM.
Detailed information for the presentation topics can be found in the 'presentation_topics.md' file.
Please get in touch with the persons responsible for the date you'll give your presentation. We want to have a meeting with each student to see that there are no major misunderstandings and to answer questions.
| Date | Topic | Student | Responsible Persons |
|---|---|---|---|
| 13.11.2023 | Bioinformatics and covid | KH | Adrian Doerr, Simon Magin |
| 13.11.2023 | Sequencing Technologies | MA | Adrian Doerr, Simon Magin |
| 13.11.2023 | Quality control (QC) | DK | Adrian Doerr, Simon Magin |
| 20.11.2023 | Trimming and filtering | JK | Adrian Doerr, Ann-Kathrin Brüggemann |
| 20.11.2023 | Alignment 1 | CH | Adrian Doerr, Ann-Kathrin Brüggemann |
| 20.11.2023 | Alignment 2 | YA | Adrian Doerr, Ann-Kathrin Brüggemann |
| 27.11.2023 | Assembly 1 | SP | Josefa Welling, Folker Meyer |
| 27.11.2023 | Assembly 2 | AA | Josefa Welling, Folker Meyer |
| 27.11.2023 | Scaffolding | MT | Josefa Welling, Folker Meyer |
| 04.12.2023 | Assembly control | HK | Alexander Thomas, Josefa Welling |
| 04.12.2023 | Variant calling | JZ | Alexander Thomas, Josefa Welling |
| 04.12.2023 | Lineage Assignment | JT | Alexander Thomas, Josefa Welling |
https://www.youtube.com/watch?v=TNKWgcFPHqw
https://www.youtube.com/watch?v=gG7uCskUOrA
https://www.youtube.com/watch?v=jX3MhWWi6n4
Dr. Simon Magin - Simon.Magin@uk-essen.de
Alexander Thomas - alexander.thomas@uni-due.de, alexander.thomas@uk-essen.de
Ann-Kathrin Brüggemann - ann-kathrin.brueggemann@uni-due.de, ann-kathrin.brueggemann@uk-essen.de
Adrian Doerr - adrian.doerr@uni-due.de, adrian.doerr@uk-essen.de
Josefa Welling - josefa.welling@uni-due.de, josefa.welling@uk-essen.de
Prof. Folker Meyer - folker.meyer@uni-due.de
Dr. Ivana Kraiselburd - ivana.kraiselburd@uni-due.de