2021 Network Modeling Virtual Summer School & Symposium

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.

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 19 – 23, 2021

Schedule

Day	AM/ PM	Theme	Instructor
1	8 – 11 AM PDT	Intro to differential equations-based biochemical modeling	Sauro
	12 – 3 PM PDT	Intro to Tellurium, libRoadRunner, Antimony and data aggregation	Porubsky
2	8 – 11 AM PDT	Model construction/ simulation	Sauro
	12 – 3 PM PDT	Parameter estimation (SBstoat)	Hellerstein
3	8 – 11 AM PDT	Model repositories, reproducibility, and databases	Smith
	12 – 3 PM PDT	Verification and validation (sbmllint)	Hellerstein
4	8 – 11 AM PDT	Cross-Validation & Design of experiments	Hellerstein
	12 – 3 PM PDT	Containerizing + distribution	Porubsky
5	8 – 11 AM PDT	8 AM: Matthias König (sbmlutils) 9 AM: Daniel Weindl (PEtab) 10 AM: Jacky Snoep	Chair: Porubsky
	12 – 3 PM PDT	12 PM: Bilal Shaikh (biosimulations) 1 PM: TJ Sego (mechanica, compucell3D) 2PM: Steve Andrews (smoldyn)	Chair: Shin