Biomedical Informatics with Sarah

Practical programming for clinicians and biologists

Elective course:
Elective course for admission to the 2nd phase of the medical exam
Field: Medical informatics
Start: October, 12th (weekly)
Estimated workload: 90-105 minutes course, 60-120 minutes at home
Capacities: max. 10
Organization: Learnweb
At: Seminar-room, Institute of Medical Informatics
(for cases of emergency a zoom-link will be provided to allow for digital participation in the course – link will be shared via Learnweb)
Language: German

Details:

Time frame:

⦁    Course: Wednesdays from 16:15 to 18:00 o´clock

  • Discussion of the home-exercises
  • New contents
  • Course-exercises considering the new contents


⦁    Home-exercises:

  • Basic tasks (processing expense 60-120 minutes): repeating the learned knowledge
  • Advanced tasks: transferring the learned knowledge to (slightly) more difficult tasks


Graded certificate of performance

Agenda:

⦁    12. October: 1. R basics (1)
⦁    19. October: 2. R basics (2)
⦁    26. October: 3. Data processing (1)
⦁    02. November: 4. Data processing (2)
⦁    09. November: 5. Visualization – standard plots
⦁    16. November: 6. Visualization – special plots
⦁    23. November: 7. Visualization – low-level plots
⦁    30. November: 8. Visualization – combined plots
⦁    07. December: 9. Excel → R → Excel
⦁    14. December: 10. Genes and proteins
⦁    21. December: 11. Genomic data in R
⦁    11. January: 12. Annotation of genomic data
⦁    18. January: 13. Analyzing sequencing data
⦁    25. January: 14. Shiny

Description:

Basic programming skills can be very practical in everyday life of a student, but also of a clinician or biologist. One can save time and avoid oversights.

Therefore, the aim of this course is to learn basic programming skills for everyday use. By the end of this course, participants should be able to identify everyday work that can be simplified and sped up by programming. Furthermore, participants should be able to perform these programming tasks on their own.

In this course, programming skills will be imparted using the programming language R. However, the focus will lie on the practical application. Examples from (bioinformatic) everyday life and exemplary data sets shall help the participants to transfer their learned knowledge to similar tasks from their everyday life. Processing of data as well as visualizing the results to generate plots for publications will take up a large part of the course content. The interaction between R and Excel is also part of this topic (import, export, formatting tables automatically etc.). Additionally, practical functions for biological and bioinformatic questions will be presented (what is the amino acid sequence of a protein? what is the effect of a mutation? benign or pathogenic? is my sequencing data of sufficient quality or will I have to repeat my experiment?). Finally, we will give a short overview of how to design websites using R shiny.

The course primarily addresses medical students. However, we are also happy to welcome interested clinicians, biologists etc.

In case you are interested: Please send a mail to Dr. Sarah Sandmann-Varghese until October, 9th2022.

Important:

Currently, we plan that our course will take place at the Institute of Medical Informatics. For cases of emergency, an additional zoom-link will be provided, to allow for digital participation in the course. In any case, an own computer is – also considering the home-exercises – strongly recommended.

Regular attendance is expected as the individual sessions build on one another.