Week Wednesday Friday Where Chapters***
09/24 Course introduction. Biochemistry basics. Modeling basics: variables, dynamical systems, kinetics. (slides video) BNS* 1, 2
10/01 Overview of systems biology modeling. Enzyme kinetics and technical modeling. BNS 3, D
10/08 Build a model: Biological background and conceptual model. Numerical solutions to differential equations. System responses. (materials video) BNS 5, 6, 7
10/15 Fitting model parameters. Debugging models. BNS  
10/22 Quantifying model quality and parameter variability. (video) Cross Validation and Bootstrapping (Videos: cross validation, bootstrapping) BNS 10
10/29 Workflow for model building. (video Jupyter-Notebook util.py test_util.py) Software standards and databases. BNS  
11/05 Standards. Model Engineering BNS  
11/12 Data Management for BioMedical Models (video) Dynamic stability and pathway motifs. BNS  
11/12 Dynamic Stability and pathway motifs. Limits to current approaches. BNS  
11/19 TBD NO CLASS. BNS  
11/26 Stochastic and Pharma models. Stochastics and Pharma models. BNS  
12/03 Student presentations. Student presentations. BNS  
  1. Homework 1 is due Oct. 24.
  2. Course project due by midnight 12/7.

*BNS is 203 Benson Hall

*** Chapters in the text book Introduction to Pathway Modeling