E340/542 Network Modeling, Lecture 1, Network Basics, Tellurium [James Glazier] August 22, 2023

ENG340/542 Biological Network Modeling Lecture 1, Introduction to Networks, Network Modeling in Tellurium and Antimony
August 22, 2023
Presented by Prof. James A. Glazier
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA

*Contents*
00:00 - Introduction
00:43 - Outline
01:32 - Course Topics--What are Networks, How can We use Biological Networks? How do We Model Them?
02:53 - What are Networks?
03:34 - Types of Networks
06:31 - Main Types of Biological Network: Chemical Reaction and Metabolic Networks, Signaling Networks, Gene Regulatory Networks, Physiologically-Based Pharmacokinetic Networks, Population Dynamics Networks, Outcome Networks
11:58 - Transdisciplinary Aspects of Networks
13:34 - Modeling in Science and Engineering: Explanation, Prediction and Control
18:14 - Course Logistics, Suggested Reference Texts (Herbert Sauro, Systems Biology, Introduction to Pathway Modeling)
27:14 - What is a Model: A Model Maps a Structure and Parameters to Measurable Results
32:23 - Networks, Nodes, States, Links
46:55 - Exercise 1.1—Build a Conceptual Network
48:07 - An Airline Route Map as a Network--What do the Nodes Represent? What are their States? What are their Links?
1:04:48 - Network Dynamics—Dynamics OF and Dynamics ON Networks
1:13:50 - Sample State Variables in Dynamic Networks
1:15:16 - Sample Dynamics on Networks
1:16:19 - Network Dynamics and Rate Laws
1:17:15 - Introduction to Chemical Reactions and Reaction Diagrams
1:20:03 - Chemical Reactions as Networks, Nodes as Species Concentrations or Amounts, Links/Arrows as Chemical Reactions
1:21:43 - Basic Concepts of Converting Chemical Reaction Diagrams into Mathematics and Simulations
1:23:52 - Chemical Reaction Rate Laws
1:28:47 - Reaction Kinetics--Chemical Reactions as Rate Equations, First-Order Ordinary Differential Equations for Concentrations
1:30:42 - Mass-Action Rate Laws
1:33:25 - Consequences of Mass Action
1:34:38 - Exercise 1.2—Implementing and Executing a Simple Chemical Reaction as an Antimony Model in Tellurium
1:36:38 - Creating a nanoHUB Account
1:38:22 - Launching Tellurium in nanoHUB
1:40:45 - Using Tellurium in Jupyter Notebooks
1:41:47 - Saving nanoHUB Notebooks
1:43:41 - Exercise 1.2.1--Your First Antimony Simulation--Cutting and Pasting from the Documentation
1:46:26 - Introduction to Antimony and Tellurium Model Specification and Execution Syntax
1:49:17 - Exercise 1.2.2--Writing and Solving the Chemical Reaction A+B goes to C at rate k*A*B
1:56:31 - Defining a Chemical Reaction and Rate Law
1:58:23 - Defining Initial Conditions and Parameter Values
2:02:54 - Format of Simulation Output
2:07:45 - Plotting Results
2:10:14 - Tuning Simulations
2:10:50 - Exercise 1.2.3--Changing Rate Constants
2:12:52 - Exercise 1.2.4/5--Changing Initial Concentrations
2:14:15 - Exercise 1.3.1—A Simple Sequential Chemical Reaction
2:16:38 - Exercise 1.4—Equilibration in Sequential Chemical Reactions

For an on-line introduction to the Antimony/Tellurium modeling framework, please see:

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