CH5016 Systems Biology for engineers


To introduce the fundamental concepts of cellular biology and biochemistry for engineering students. To reconstruct small scale biochemical reactions networks, and to apply constraint-based modeling methods to decipher network properties. To perform simple simulations (flux balance analysis, flux variability analysis, phenotypic phase plane analysis, gene deletion, etc.) to simple networks like E.coli core model. To relate and answer simple biological questions from the in silico results. To introduce open questions in the area and propose novel modeling algorithms.

Course contents:

1. Introduction to cellular biology and biochemistry with engineering perspective
2. Basic concepts of systems biology
3. Cellular networks: metabolic, transcriptional, and signaling networks
4. Stoichiometric matrix: fundamental subspaces
5. Introduction to concept of constraints
6. Reconstruction of biochemical reaction networks
7. Overview of existing constraint-based reconstruction methods
8. Modeling biochemical reconstructions
9. Applications of constraint-based metabolic models
10. Overview of existing human metabolic networks, and cell-specific constraint-based metabolic models