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.
Thursday, January 29, 2015
SysBio15 Asgn_8A_Class_08_Article_10_2015_01_29
Classical Network Models: Read Article 10 J. J.
Tyson, A. Csikasz-Nagy, and B. Novak. The dynamics of cell cycle
regulation. BioEssays 24 (12):1095-1109, 2002.. We will discuss this
article in depth, which will take at least a full class. This should be a
first reading to get an overview. Post a PCRC. We will have a second,
more careful reading in a second class with a second PCRC.
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James Pino
ReplyDeleteAsgn_8A
0: Knew basics of cell cycle control. Knew the use of mathematical modeling in biology.
1:Learned more precise details about the players controlling the cell cycle. The mutant models were capable of recreating experimental findings.
2: Pressing: What type of experimental data do you compare the model?
3: Presentation: Examples of biological drive experiments
4: Thoughts: Modeling biology seems fun
Cameron Togrye
ReplyDeleteAsgn 8A / Dynamics of Cell Cycle Regulation
0. Knew: The existence of cell cycle checkpoints which check for criteria like properly replicated DNA and cell size.
1. Learned: How to understand and analyze bifurcation diagrams, especially in their use with signal vs response bifurcation diagrams.
2. Pressing: What is the purpose of the oscillatory jumps which trigger mitosis? Why cant it be a switch like the other checkpoints?
3. Presentation: Examples of Cells which deviate from the presented standard cell cycle
4. Thoughts: Why is it that complexes evolve in these regulatory checkpoints instead of a single protein? What advantages does this present?
Chuck Herring
ReplyDeleteAsgn_8A
0: Knew: Generally knew about the cell cycle and mathematical modeling in biology.
1: Learned: A better understanding of bifurcation diagrams.
2: Pressing: Could an unstable area represented in a bifurcation diagram become stable if more knowledge/components is/are added?
3: Presentation: An example of how mathematical modeling can lead to a better understanding of biology.
4: Thoughts: What sizes are these types of models (ODE/PDE) limited too? The authors say 10-50 were used, at what point does having too many equations become an over-fitting issue?
Zach Bednarke
ReplyDeleteAsgn 8a
0: Knew: Very basics of the cell cycle
1: Learned: How bifurcation theory can provide a useful (nontrivial) qualitative analysis of a nonlinear system.
2: Pressing: Can we unify bifurcation diagrams with phase space diagrams to make the information of both visible on one graph?
3: Presentation: How Problem Solving Environments aid in removing trial and error from model construction.
4: Thoughts: What were the analytical chemistry techniques used by Tyson et al to measure concentrations of the various proteins at precise times throughout the cell cycle?
Cami Johnson
ReplyDeleteAssignment 8A: Article 10
0. Knew: The basics of the cell cycle and the use of mathematical models in systems biology.
1. Learned: How to read bifurcation diagrams
2. Pressing ?: What is the limit for where bifurcation diagrams can accurately describe a system?
3. Presentation: Other applications of mathematical modeling in biology
4. Thoughts: Class Thursday really cleared up most of the confusion for me in this paper. Hopefully class today will help me make sense of the next paper.
Mark Vander Roest
ReplyDeleteAssignment 8A
0. Knew: Basics of cell cycle regulation and thresholds for continuing in the cell cycle.
1. Learned: Bifurcation diagrams, specific molecular regulators of the cell cycle.
2. Pressing ?: Can an unstable steady state be reached and held or are cells too dynamic?
3. Presentation: Applications of modeling to describe biological phenomena.
4. Thoughts: I'm interested in seeing the use of more complex models to predict unobserved cellular processes.
Kendra Oliver
ReplyDeleteAssignment 8A
0: Knew: Generally knew about the cell cycle and regulation mechanisms.
1: Learned: Better understanding of bifurcation diagrams. Modeling of cell cycle components. Some of the benefits of modeling compared to experimentation.
2: Pressing: In a novel system, how to you determine the independent versus dependent variable by which you are going to develop your model? How do you add more variables and what is the limit of this modeling?
3: Presentation: Example of forming a model using a different simple system.
4: Thoughts: An example of predictive models would be really interesting but I think that you would need to have a non-trivial amount of information about the system before the model is informative. What are the current ways that proteins can group to look at high correlation between protein subtypes?
Kate Jones
ReplyDeleteAssignment 8A
0. Knew: The basics of the cell cycle and the role of cyclin at checkpoints during cell cycle regulation. I knew some of the biology but not much of the mathematical modeling approach.
1. Learned: A series of bifurcation diagrams can display the progression of yeast through the cell cycle as they fluctuate between stable states. Mathematical modeling creates these diagrams.
2. Pressing ?: I definitely needed help reading the bifurcation diagrams before class. Going through the ball on the seesaw example helped me better understand the steady states and unstable equilibrium.
3. Presentation: I think that going through the figures was a good way to understand the importance of this article
4. Thoughts: I was able to understand the bifurcation diagrams when I thought of the steady states in terms of hills and troughs. If the equilibrium is unstable, it acts like a ball on the top of a hill in that any type of disturbance will send the ball down the hill. If it is stable, it may go up the side of the hill slightly but returns to the valley.