The Center for Reproducible Biomedical Modeling develops workshops alone and in collaboration with several academic organizations and conferences in order to disseminate educational material focused on the practical use of modeling software and theoretical explorations of modeling theory. An archive of workshop materials, which includes videos and links to code, data, and model repositories, along with advertisements for upcoming workshops, is maintained below.
2020 Network Modeling Virtual Summer School & Symposium
By the end of this week-long course, participants will have learned how to construct, simulate, and validate a biochemical differential equation-based model using the model development package, Tellurium, and programming in Python. Post-course support and collaboration will be available to continue simulation development.
Dates: July 27 – 30, 2020
Schedule
| Day | AM/ PM | Theme | Instructor |
|---|---|---|---|
| 1 | 8 AM PDT | Intro to differential equations-based biochemical modeling | Porubsky |
| 12 PM PDT | Intro to Tellurium, libRoadRunner, Antimony and data aggregation | Porubsky | |
| 2 | 8 AM PDT | Model construction/ simulation | Sauro |
| 12 PM PDT | Parameter estimation | Sauro | |
| 3 | 8 AM PDT | Advanced simulation and analysis | Sauro |
| 12 PM PDT | Verification and validation | Hellerstein | |
| 4 | 8 AM PDT | Model repositories and distribution | Lucian, Somogyi |
| 12 PM PDT | Choose one of the following options: Containerizing simulations w/ Docker Advanced topics in model fitting |
Porubsky Sauro |
|
| 5 | 8 AM PDT | Optional hacking | Sauro, Porubsky, other tutors |
| 12 PM PDT | Optional hacking | Sauro, Porubsky, other tutors |
