The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
Wednesday, October 9, 2019
SysBio19 Asgn_3_Class__Tyson_article
Browse Tyson article Modeling the dynamic behavior of biochemical
regulatory networks. Scan this article to familiarize yourself with the
contents. Answer the questions: 1) What did you already know? 2) What
did you learn? 3) What is your most pressing question that you would
like Kyle to explain in class? 4) How does this relate to your project?
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1) What did you already know?
ReplyDeleteI knew of some of the ways that they used to model temporal changes in behavior such as boolean networks and piece-wise functions.
2) What did you learn?
I learned several different types of modeling like heaviside ode model. I never really though about the use of the heaviside function outside of circuits.
3) What is your most pressing question that you would like Kyle to explain in class?
Which models has he looked into/ found success with in terms of dopaminergic neurons?
4) How does this relate to your project?
This paper just provides many different ways to model behavior and this would help in terms of understanding dopaminergic neurons. This paper is also very nice in that it says positive and negative of each model allowing for better selection for the project.
Which models has he looked into/ found success with in terms of dopaminergic neurons?
DeleteI haven't done anything too extensive with all the models and still need to fully develop the boolean framework for the problem.
1) Knew: Different types of mathematical modeling applied to biology (ODE, boolean, stochastic)
ReplyDelete2) Learned: "Poorly characterized systems should be modeled by methods that can be implemented quickly, with minimal requirements for mechanistic details, and that pro- vide general, qualitative insights that can be useful in guiding our intuition about the control system and designing the next set of experiments to be pursued. Well characterized systems should be modeled by accurate methods that provide reliable, quantitative behaviors of the hypothetical control systems; properties that can be compared in detail to observed cellular behaviors and that pro- vide rigorous, testable predictions for future experiments"
3) Question: What is the most popular modeling method for cellular differentiation/de-differentiation?
4) Project: This review is very useful in helping us choose the resolution needed in the mathematical models of our systems of interest.
What is the most popular modeling method for cellular differentiation/de-differentiation?
DeleteThere isn't really a standard model that has been established yet and I cannot find any resources describing which models are more popular than others. Boolean networks is one of the more easily accessible models when compared to most methods so there is a good chance it is more popular.
1) What did you already know?
ReplyDeleteMost of the methods mentioned.
2) What did you learn?
There is a bifurcation called saddle node on an invariant circle.
3) What is your most pressing question that you would like Kyle to explain in class?
NA
4) How does this relate to your project?
Understanding the available modeling methods is important for creating models.
1) What did you already know?
ReplyDeleteI knew about some of the different types of modeling regulatory networks that they talked about such as boolean networks, differential equations, etc. I did not know much about the specific details about each of these methods though.
2) What did you learn?
I learned the math behind some of these methods. I also had not used SDEs before. I appreciated Table 4 in which the authors clearly explain the types of bifurcation points.
3) What is your most pressing question that you would like Kyle to explain in class?
4) How does this relate to your project?
There are many ways you can model the biological pathways that are used to modify stromal to iPSC transitions. We would need to obtain data on the varying concentrations of certain factors and rates of change of some gene expression, but we could compare different modeling techniques on these pathways.
1) What did you already know?
ReplyDeleteThe concepts of biochemical regulatory networks and feedback loops are familiar to me
2) What did you learn?
The mathematical descriptions of these regulatory networks are a new concept to me. I appreciated the use of mathematics to drive pathway description.
3) What is your most pressing question that you would like Kyle to explain in class?
How do these equations and mathematics relate to the constructed relationship maps?
4) How does this relate to your project?
I want to be able to predict cell function in different states and with different biochemical regulation. These models will give me the tools to do so more accurately.