E443/543 Virtual Tissues: Lecture 13: Networks and Cells, April 9, 2024

ENG443/543 Multicellular Virtual Tissue Modeling, Lecture 13, April 9, 2024
Integrating Network Models in CC3D Cells, Modeling Delta-Notch Signaling

Presented by James A. Glazier
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA

Slides and exercises available on request.

*Detailed Contents*
Last Time
Introduction to Network Modeling
Chemical Reaction, Signaling, Gene Regulatory and Physiological Networks
Antimony Syntax
Integrating Antimony and CC3D
Loading Antimony Models
Reading and Writing Antimony Variables and Parameters
Time-Stepping Antimony Models
Exercise 13.1: Loading and Antimony Model into Individual Cells
Exercise 13.2: Changing Rate Constants in Antimony Models Cell-by-Cell
Exercise 13.3: Delta-Notch Patterning
Exercise 13.4: Using Steering Panels in CompuCell3D

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