ENG443/543 Virtual Tissues Lecture 1, Introduction to Virtual Tissues and CompuCell3D, Jan 10 2023

ENG443/543 Computational Bioengineering Multicellular Virtual Tissue Modeling Lecture 1, January 10, 2023

Introduction to Virtual Tissues and CompuCell3D

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

Slides and exercises available on request.

Detailed Outline:
Class Organization
Tentative Schedule
Reference Materials
Why do we need quantitative computational models in biology/biomedicine?
Introduction to Multicell Modeling (Virtual Tissues)
Multicell Methodologies
CompuCell3D Environment and Core Concepts
Exercise 1.1 Running an Angiogenesis Simulation in CC3D on nanoHUB
Exercise 1.1.1 Running a Simulation in Player
Exercise 1.1.2 Controlling Visualization of Cells in Player
Exercise 1.1.3 Visualizing Chemical Fields in Player
Applications of Virtual Tissues
Drosophila Wing Patterning and Delta-Notch-mediated Cell Cycle
Cell Crawling
Vascular Tumors, Somatic Evolution in Tumors
Choroidal neovascularization in Age-Related Macular Degeneration
Mechanisms of Embryonic Segmentation
Polycystic Kidney Disease
Limb Bud Growth
Viral Infection, Immune Modeling and Antiviral Therapy
Diabetic Retinopathy
Liver Toxicity
Viral Infection and Immune Response
Exercise 1.2 Thinking about Modeling Projects
Exercise 1.3 Writing and Running a CC3D Model of Cell Growth and Division Using Twedit++ Wizard
Exercise 1.3.1 Launching Twedit++ and Using Wizard to Create a Simulation
Exercise 1.3.2 Launching Player from Twedit++
Exercise 1.3.3 Changing Parameters to Explore a Simulation
Architecture of CC3D Simulation Specifications
CC3DML and Python Steppables
CC3DML
Metadata and Potts Blocks (Parallelization and Domain Properties)
Cell Type Specification
Contact Energy Specification
Initial Condition Specification
CC3D Python
Start Function
Cell-list Iterators and Cell Attributes
Cell Initialization
Step Function
Cell Growth
Cell Division
Cloning and Inheritance of Attributes

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