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 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, are maintained below.
2022 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 18 – 22, 2022
Schedule
| Day | AM/ PM | Theme | Instructor |
|---|---|---|---|
| Monday 7/18 |
8 AM – 12 PM PDT | Intro to differential equations-based biochemical modeling
Intro to Tellurium, libRoadRunner, Antimony |
Sauro Shin |
| Tuesday 7/19 |
8 AM – 12 PM PDT | Model construction/ simulation
Parameter estimation (SBstoat) |
Sauro Hellerstein |
| Wednesday 7/20 |
8 AM – 12 PM PDT | Source control and model repositories
Verification and validation (sbmllint) |
Smith Hellerstein |
| Thursday 7/21 |
8 AM – 12 PM PDT | Reproducibility and standard formats
Time to review all material covered in previous sessions, open for questions |
Porubsky all instructors |
| Friday 7/22 |
8 AM – 12 PM PDT | Matthias König
Paul Macklin Jonathan Karr James Glazier |
Porubsky & Shin chair symposium |
Time (and timezone) breakdown:
8 AM PDT [11 AM EDT | 5 PM CEST] – 12 PM PDT [3 PM EDT | 9 PM CEST]
2022 Network Modeling Summer School & Hackathon
Click photo to download flyer.
