Slides & Exercises

BiomeFUN_2025

Advanced course in Serbia

In this course, I introduced two types of models that are useful for studying microbial communities.
The material combines conceptual overviews with practical examples, giving participants hands-on experience with different modeling approaches.

• Theoretical Models in Microbial Ecology
  • Lecture (PPTX)
  • Exercises
    • Exercise 1 - LV models
    • Exercise 2 - Consumer-resource models
• Metabolic Flux Analysis
  • Lecture (PPTX)
  • Exercises
    • Exercise 1 - Basic stoichiometric models
    • Exercise 2 - COBRA intro
      • Required file: Basic model (Excel)
    • Exercise 3 - E. coli core model
      • Required file: E. coli core JSON

Analysis of Metabolic Networks (readers)

MSc Life Sciences and Technology - TU DELFT

Below you can find the teaching materials for my course in the MSc Life Sciences and Technology program at TU Delft.
The readers introduce key concepts in metabolic modeling, including mass balances, stoichiometric models, and pathway thermodynamics.

• Reader M0: Definitions - PDF
• Reader M1: Rates & balances - PDF
• Reader M2: Stoichiometric modeling - PDF
• Reader M3: Pathway thermodynamics - PDF