The Center for Reproducible Biomedical Modeling develops tutorials in order to disseminate educational material focused on the practical use of modeling software and theoretical explorations of modeling theory. An archive of tutorial materials, which includes but is not limited to videos and links to code, data, and model repositories is maintained below.

Tutorials

Winter 2023 Schedule

Day AM/ PM Theme Instructor
Wednesday
2/8/23
2 PM – 3 PM PDT Introduction to particle-based modeling in Tissue Forge T.J. Sego
Wednesday
2/8/23
3 PM – 4 PM PDT Introduction to parameter fitting using roadrunner and Julia Michael Kochen
Wednesday
3/8/23
2 PM – 3 PM PDT Introduction to spatial modeling Steve Andrews
Wednesday
3/8/23
3 PM – 4 PM PDT  Modeling neurological systems with recurrent neural networks in Python Veronica Porubsky

Fall 2022 Schedule

Day AM/ PM Theme Instructor
Wednesday
11/9/22
2 PM – 3 PM PDT Intro to Tellurium Lilly Tatka
Wednesday
11/9/22
3 PM – 4 PM PDT Using Antimony: Introductory and Advanced Lucian Smith
Wednesday
12/7/22
2 PM – 3 PM PDT Introduction to metabolic control analysis Janis Shin
Wednesday
12/7/22
3 PM – 4 PM PDT Visualizing reaction networks using SBMLDiagrams Jin Xu

The tutorial series will happen twice per quarter. If you are interested in the practical use of modeling software and theoretical explorations of modeling theory, please do not hesitate to join us. Please join the Google group Cell-Modeling Seminar for further notifications of the Sauro lab tutorials.

Please also let us know if you have any advice to improve the tutorials.

Jin Xu and Herbert M. Sauro organize the tutorial series. Hunter Robbins maintains the website. We appreciate the generous financial support of NIH U24-EB028887.

Tutorials Archive

Intro to Tellurium
Lilly Tatka

November 9, 2022

Using Antimony
Lucian Smith

November 9, 2022

Intro to Metabolic Control Analysis
Janis Shin

December 7, 2022

Visualizing Reaction Networks Using SBMLDiagrams
Jin Xu

December 7, 2022

Intro to particle-based modeling in Tissue Forge
T.J. Sego

February 8, 2023

Intro to parameter fitting using roadrunner and Julia
Michael Kochen

February 8, 2023