E340/542 Network Modeling, Lecture 1, Network Basics, Tellurium [James Glazier] August 27, 2024

ENG340/542 Biological Network Modeling Lecture 1, Introduction to Networks, Network Modeling in Tellurium and Antimony
August 27, 2024
Presented by Prof. James A. Glazier
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA

Engineering 340/542 teaches how to model network dynamics using the Tellurium/Antimony model specification framework and Python-based Jupyter notebooks. The course covers the basics of developing simple metabolic, cell-signaling, gene-regulatory and pharmaco-kinetic network models and fitting models to experimental data. The first lecture introduces the basic concepts of networks: nodes, node states, links and interactions. What are the types of network? What are dynamic networks, where do we find them and how can we represent them and apply them? The class ends showing how to create and run a very simple example of an chemical reaction model in Colab. Since Colab is a free resource, anyone who is interested can create a Colab account and learn along with us.

*Contents*
00:00 - Introduction
- Outline
- Course Topics--What are Networks, How can We use Biological Networks? How do We Model Them?
- What are Networks?
- Types of Networks
- Main Types of Biological Network: Chemical Reaction and Metabolic Networks, Signaling Networks, Gene Regulatory Networks, Physiologically-Based Pharmacokinetic Networks, Population Dynamics Networks, Outcome Networks
- Transdisciplinary Aspects of Networks
- Modeling in Science and Engineering: Explanation, Prediction and Control
- Course Logistics, Suggested Reference Texts (Herbert Sauro, Systems Biology, Introduction to Pathway Modeling)
- What is a Model: A Model Maps a Structure and Parameters to Measurable Results
- Networks, Nodes, States, Links
- Network Dynamics—Dynamics OF and Dynamics ON Networks
- Sample State Variables in Dynamic Networks
- Sample Dynamics on Networks
- Network Dynamics and Rate Laws
- Introduction to Chemical Reactions and Reaction Diagrams
- Chemical Reactions as Networks, Nodes as Species Concentrations or Amounts, Links/Arrows as Chemical Reactions
- Basic Concepts of Converting Chemical Reaction Diagrams into Mathematics and Simulations
- Chemical Reaction Rate Laws
- Reaction Kinetics--Chemical Reactions as Rate Equations, First-Order Ordinary Differential Equations for Concentrations
- Mass-Action Rate Laws
- Consequences of Mass Action
- Exercise 1.2—Implementing and Executing a Simple Chemical Reaction as an Antimony Model in Tellurium
- Using Tellurium in Jupyter Notebooks
- Exercise 1.2.1--Your First Antimony Simulation--Cutting and Pasting from the Documentation
- Introduction to Antimony and Tellurium Model Specification and Execution Syntax
- Exercise 1.2.2--Writing and Solving the Chemical Reaction A+B goes to C at rate k*A*B
- Defining a Chemical Reaction and Rate Law
- Defining Initial Conditions and Parameter Values
- Format of Simulation Output
- Plotting Results
- Tuning Simulations
- Exercise 1.2.3--Changing Rate Constants
- Exercise 1.2.4/5--Changing Initial Concentrations
- Exercise 1.3.1—A Simple Sequential Chemical Reaction
- Exercise 1.4—Equilibration in Sequential Chemical Reactions

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

If you found this video useful, please check out our other videos teaching computational modeling: