ENG340/542 Network Modeling, Lecture 2, Types of Biological Network [James Glazier] August 29, 2023

ENG340/542 Biological Network Modeling Lecture 2, Types of Biological Network, Thinking about Networks
August 29, 2023
Presented by Prof. James A. Glazier
Indiana University, Department of Intelligent Systems Engineering and Biocomplexity Institute
Bloomington, IN 47408, USA

Main Reference: Herbert Sauro, Systems Biology: Introduction to Pathway Modeling, Chapter 1

*Contents*
0:00:42 - Learning Objectives
0:04:53 - Readings and Resources
0:06:12 - Reviews of Network Applications and Fundamental Concepts: Nodes, States and Links, Types of Arrow
0:11:04 - Review: Writing and Interpreting Chemical Reactions as Networks of Rate Equations
0:12:36 - Review: Defining and Simulating Chemical Reactions Using Antimony and Tellurium
0:15:21 - Repositories of Biological Networks: KEGG, BioModels
0:18:46 - Metabolic, Signaling and Gene Regulatory Networks and Their Timescales
0:26:41 - Metabolic Networks, Function,
0:29:30 - Questions to Ask about a Metabolic Network
0:36:14 - Metabolic Network Notation, Interpretation
0:39:16 - Catalysis and Its Interpretation
0:44:57 - Exercise 2.0.1: Find a Metabolic or Chemical Reaction Network Model and Explain It
1:03:25 - Spatial Complexity of Metabolic Networks
1:06:17 - Signaling Networks, Function, KInases
1:13:37 - Questions to Ask About Signaling Networks
1:17:01 - Signaling Network Notation
1:19:06 - Interpretating Signaling Networks as Rate Laws, Activation and Inhibition
1:22:41 - Spatial Considerations for Signaling Networks
1:24:55 - Common Mechanisms in Signaling Networks, Complex Formation, Phosphorylation and Dephosphorylation, Targeted Degradation
1:27:19 - Exercises 2.0.2: Find a Signaling Network Model and Explain It
1:38:13 - Gene Transcription into RNA and RNA Translation into Protein (Central Dogma of Biology)
1:45:26 - Gene Regulatory Networks, Function
1:51:09 - Questions to Ask about Gene Regulatory Networks: Boolean vs Rate Models
2:12:05 - Gene Regulatory Network Notation, Types of Nodes and Arrows
2:17:32 - Complications in Interpreting Gene Regulation as Networks
2:19:09 - Turning Gene Regulatory Network Diagrams into Rate Equations
2:26:02 - Gene Regulatory Network Motifs: Cascades, Autoinhibition, Modulation
2:28:35 - Exercise 2.0.3: Find a Gene-Regulatory Network Model and Explain It

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