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
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. 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 on the nanoHUB deployment of Tellurium (https://nanohub.org/resources/tellurium). Since nanoHUB is a free resource, anyone who is interested can create a nanoHUB account and learn along with us.
Presented by Prof. James A. Glazier
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA
Slides available at: https://drive.google.com/drive/folders/1fPuIrK-cQq4COZ4JnnHE4fFJQhvRV3Yq?usp=sharing
Exercises available at: https://drive.google.com/drive/folders/1YZEqb2_s9sYuogs4GZ23Xw13gVtyipH_?usp=sharing
Demos available at: https://drive.google.com/drive/folders/1fRM27czpGNZfJIh1JAhtDLSmDAKwNlds?usp=sharing
*Contents*
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
If you found this video useful, please check out our other videos teaching computational modeling:
For dynamic network modeling: https://www.youtube.com/playlist?list=PLiEtieOeWbMKSwbYZ6T6ywBruoHNazcFk
For multicellular agent-based modeling: https://www.youtube.com/playlist?list=PLiEtieOeWbMJTch7kleSZxkM06bLoYm7i
source
