ENG443/543 Virtual Tissues Lecture 14 Network Models April 19 2022

ENG443/543 Virtual Tissues Lecture 14 Network Models April 19 2022

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

Student Project Presentations
Last Time—Introduction to Network Modeling
Chemical Reaction Networks, Signaling Networks, Gene Regulatory Networks, Physiologically Based Pharmacokinetic Models
ODE Network Representations
Antimony Model Specification Syntax
Functional Assignments in Antimony
Connecting Antimony Models with CC3D via Python
Loading Antimony Models
Into Cells
Free Floating
Time Stepping Antimony Models
Reading and Writing Antimony Model Variables
Deleting and Copying Antimony Models
Multiscale Modeling: reaction kinetic models + CC3D
Exercise 14.1: Load Free Floating Antimony Model into CC3D
Exercise 14.2: Load Antimony Model into Cells
Delta-Notch: Biological Background and Mathematical Model
Exercise 14.3: Implementing Delta-Notch in CC3D
Exercise 14.4: Steering Delta-Notch Parameters on the Fly