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.

Tellurium User Training Workshop

By the end of this week-long course, participants will have learned how to construct, simulate, and validate a biochemical differential equations-based model using the model development package, Tellurium, and programming in Python. Participants will also explore building a Docker container to distribute their model and simulation studies. An optional hacking day will be provided so that participants can consult the tutors on how skills learned in the course can be applied to their biological problem of interest.  Post-course support and collaboration will be available to continue simulation development.

Additional information available on the CompuCell3d website: https://compucell3d.org/Workshop20

Dates

July 27 – 31, 2020

Schedule

Day AM/ PM Theme Instructor
1 AM Intro to differential equations-based biochemical modeling and data aggregation Porubsky, TBD
PM Intro to Tellurium, libRoadRunner, and Antimony Porubsky, TBD
2 AM Model construction Sauro, TBD
PM Parameter estimation Sauro, TBD
3 AM Advanced simulation and analysis Sauro, TBD
PM Verification and validation Sauro, TBD
4 AM Containerizing simulations with Docker Porubsky, TBD
PM Publishing reproducible models Porubsky, TBD
5 AM Optional hacking Sauro, Porubsky
PM Optional hacking Sauro, Porubsky

Github Repositories

Tellurium and libRoadRunner tutorial