ENG340/542 Network Modeling Lecture 1, Basics of Networks, Tellurium, August 23, 2022

ENG340/542 Computational Bioengineering Network Modeling Lecture 1, August 23, 2022
Introduction to Networks, Network Modeling in Tellurium and Antimony

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:
What are Networks?
Types of Networks
Main Types of Biological Network
Modeling in Science and Engineering
Course Logistics
What is a Model
Networks, Nodes, States, Links
Airline Route Map as a Network
Exercise 1.1—Build a Conceptual Network
Network Dynamics—Dynamics OF and Dynamics ON Networks
Chemical Reactions
Arrow Notation
Rate Laws
Mass-Action Rate Laws
Reaction Kinetics
Using nanoHUB
Tellurium Modeling Environment
Exercise 1.2—Implementing and Executing a Simple Chemical Reaction as an Antimony Model in Tellurium
Exercise 1.3—A Simple Sequential Chemical Reaction
Exercise 1.4—Equilibration in Chemical Reactions

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