ENG340/542 Network Modeling: Lecture 7, Motifs, Phase Portraits [James Glazier], October 3, 2023

ENG340/542 Biological Network Modeling Lecture 7, Translating SBML to Antimony, Using Tellurium in Colab, Student Projects, Thinking About Models
October 3, 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

*Contents*
00:31 - Outline
01:25 - Suggest Topics for Clarification
12:11 - Step 1 Navigate to Tool, Step 2 Search for Desired Model Topic
12:27 - Step 3 Select Model to Translate, Step 4 Download Model
13:00 - Steps 5 and 6 Translate Again if Needed. Save or Copy Antimony Model
14:06 - Step 7 Paste Antimony Model into Tellurium Execution Script and Execute
20:11 - Exercise 7.2 Use MakeSBML to Download and Run a Model of Your Choice
20:44 - Student Choices and Strategies for Debugging Auto-translated Antimony Models, Looking for Illegal Variable Names, Tuning Time Steps
33:09 - Annotations in Antimony and Principles of Annotation
37:35 - Introduction to Compartments
43:08 - Exercise 7.3 Using Variable Stoichiometry in Antimony to Change the Exponent in the Hill Equation
47:18 - Using := to implement continuous assignment in Antimony
51:47 - Student Project Presentations
52:29 - William Cesaretti: Modeling P53 and DNA Damage, P53 Oscillations and Bifurcations
54:20 - Discussion and Analysis of the Model
1:02:44 - Hill Function Representation of Gene Regulatory Networks
1:05:27 - Representing Transport
1:18:31 - Elmar Bucher: Gene Regulation During Myeloid Differentiation, Biology
1:24:17 - Boolean Networks
1:29:41 - Differences between Behavior of Boolean and Reaction Versions of the Network
1:44:15 - Designing Network Functions
1:46:19 - Differential Measurements in Biology
1:50:19 - Questions We Can Ask and Answer Using Networks
1:54:32 - Qualitative Questions
1:59:55 - Phase Diagrams
2:04:54 - Semi-Quantitative Questions
2:13:56 - Quantitative Questions
2:17:33 - Exercise 7.4 Thinking About Questions to Ask for Your Networks
2:24:49 - Discussion of Different Styles and Philosophies of Mathematical Biology

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