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_8B_Class_08_Article_11_2015_01_29
Classical Network Models: Read very carefully Article
11 J. J. Tyson, K. C. Chen, and B. Novak. Sniffers, buzzers, toggles
and blinkers: dynamics of regulatory and signaling pathways in the cell.
Curr.Opin.Cell Biol. 15 (2):221-231, 2003.. Also read PPT-10 for for a
compact summary. We will discuss this article and the PPT 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 for Thursday.
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Cameron Togrye
ReplyDeleteAsgn_8B / Sniffers, buzzers, toggles and blinkers
0. Knew: The role of cyclin dependent kinases on the regulation of cell proliferation via the cell cycle.
1. Learned: The various motifs of control that exist within cellular regulatory and signaling pathways (one way switches, reversible switches, etc.)
2. Pressing: Can cooperative binding also account for the sigmoidal response curve in Figure 1c. The paper states such a curve is the result of michaelis-menten kinetics, but these curves normally give a velocity which is more similar to the hyperbolic curve of the paper.
3. Presentation: Examples in the body in which each control motif is employed
4. Thoughts: Are there variations on the perfect adaptation signal response curve that do not feature diminished response levels? It seems like this would be a control mode that could be favorable in some physiological scenarios.
Chuck Herring
ReplyDeleteAsgn_8B
0. Knew: General knowledge of protein networks and dynamics.
1. Learned: The dynamics of mutual activation, mutual inhibition, and homeostatics were new to me.
2. Pressing: In 1(d) how is R independent of S?
3. Presentation: Examples of network dynamics that are relevant to biological systems.
4. Thoughts: Given the difficulties and time required to build kinetic models, how will we incorporate these into our rapid response plan?
Juan Gnecco
ReplyDeleteAsgn_8B
0. Knew: Basic basic basic concept behind bifucartion diagrahms
1. Learned how different aspects of biology in terms of feed back/forward mechanisms can be modeled and how complex they can quickly get.
2. Pressing: How do we "read" a bifucaration diagram specially when it describes an oscilating or heresis.
3. Presentation: different forms of dynamics modeled by bifurcations.
4. Thoughts is the same trend followed for any cycle in biology? or is each one individual.
Cami Johnson
ReplyDeleteAssignment 8B: Article 11
0. Knew: Mathematical models can be useful in describing biological systems
1. Learned: How to describe some of the building blocks of these models, like sniffers, buzzers, toggle switchers, and oscillators.
2. Pressing ?: I'd really appreciate a good explanation of the second column of Figure 2.
3. Presentation: Examples of sniffers, buzzers, toggles, and blinkers in biology
4. Thoughts: I think I understood the essentials of this paper, but I think class discussion today will really help me understand it better.
Mark Vander Roest
ReplyDeleteAssignment 8B
0. Knew: The utility of mathematical models for describing and predicting biological processes.
1. Learned: The ways that certain pathways can be viewed almost as circuit elements and control mechanisms.
2. Pressing ?: What on earth is happening with some of those cyclic mechanisms?
3. Presentation: Different mechanisms of control and the way that they're modeled.
4. Thoughts: I'm starting to see how principles of abstraction may still capture the necessary details of a biological system. Cool stuff.
Kendra Oliver
ReplyDeleteAssignment 8B
0. Knew: Mathematical models can be useful in describing biological systems. But, am still unclear the protocol for the models development.
1. Learned: Building an equation for a biological model. There are multiple components that can be used to build it such as oscillators.
2. Pressing ?: Still unsure about the actual protocol for developing a model. Is there a specific set of steps (set order) to developing a mathematical model for a biological system? What are these step? When are you over modeling?
3. Presentation: 10 steps to building a mathematical biological model.
4. Thoughts: Still do not have a complete understanding but am slowly getting the idea.
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ReplyDeleteKate Jones
ReplyDeleteAssignment 8B
0. Knew: Mathematical models can help us understand the system through protein interactions in response to signals. I understood how negative and positive feedback would look on a graph.
1. Learned: Before class, I was lost on the oscillators sections. However, I think I have a little bit of a better understanding now that we have gone through the articles.
2. Pressing ?: I still need a little help understanding some of the graphs with the directional arrows (plane phase diagrams i think??)
3. Presentation: I am glad that we took time to go through the diagrams of these articles because I think the graphical representation is confusing but extremely helpful once you understand what you are looking at.
4. Figure 2 a reminded me of hormone cycles and how the body responds to an increase in one hormone in order to increase or decrease production of another. This prior knowledge helped me understand how x, yp, and rp were related