Syllabus
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 |
- Homework 1 is due Oct. 24.
- Course project due by midnight 12/7.
*BNS is 203 Benson Hall
*** Chapters in the text book Introduction to Pathway Modeling