Session 1 Introduction to system analysis

Session 2 Quick start with R

• Bacterial count data (Text file)
• R Script (Text file)

Session 3 The continuous flow stirred tank reactor

Session 4 Residence times

• Auxiliary R Script (Text file)

Session 5 First order processes

• Lake data set (Text file)

Session 6 Simultaneous ODE

Session 7 Limitation and inhibition

• Experiment 1, Algae data (Text file)
• Experiment 1, Blank data (Text file)
• Experiment 2, Algae data (Text file)
• Experiment 2, Blank data (Text file)
• Analysis of experiments (R script file)

Session 8 Matrix-based notation for ODE (rodeo package)

• Epidemic model 1 (.xlsx workbook for use with "rodeo")
• Epidemic model 2 (.xlsx workbook for use with "rodeo")

Session 9 Bioreactor model (E. coli on LB)

• Bioreactor model (.xlsx workbook for use with "rodeo")

Session 10 Competition and coexistence

• Utility functions for model analysis (R code)
• Single species bioreactor model (.xlsx)
• Two species bioreactor model, basic version (.xlsx)
• Two species bioreactor model, variable forcings (.xlsx)
• Two species bioreactor model, including predation (.xlsx)
• Two species bioreactor model, with biofilm (.xlsx)

Session 11 Energy balance (penguin example)

Introduction on concentration-response curves

• Lecture slides

Lab course: Bacterial fitness under antibiotic exposure

• Reference dataset (.xlsx)
• Student dataset from 2026 (.xlsx)
• Theory and R code for data analysis

Material will appear before the course starts.

These are collections of personal recommendations, not strict guidelines.

• Presentations (HTML, in German)
• Writing (PDF, in English)

• Course material (.zip archive) ! about 130 MB

• Presentation (.pdf)
• Data (.zip archive)

Short version (recommended)

• Presentation (.pdf)
• Data (.zip archive)

Long version (to be updated)

• Presentation (.pdf)
• Data (.zip archive)

• Presentation (.pdf)

• Presentation (.pdf)

• Intro to ODE-based modeling
• Hands-on part (R/rodeo)