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.
0. Knew the basics of modeling but had no real understanding into the role of Guyton-Coleman in the development of models as a whole.
ReplyDelete1. What I found insightful was the description of how one validates a model...especially in terms of qualitative, quantitative by steady state, and quantitative by dynamic. I think the distinguish between the steady state and dynamic quantification is important to understand because just because a model is good in one condition does mean much if it can not hold up to perturbations.
2. How does the Guyton-Coleman model hold up when under perturbation? Are all of the variables accurately modeled or are some less important?
3. Guyton-Coleman 101.
4. I found the overall description of the modeling process and the application to systems biology insightful as it provided perspective on how techniques evolved.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_14A_Class_18_Article_22_2013_10_24
0. Knew: Earlier version of Guyton-Coleman.
1. Learned: Effect of pneumothorax on cerebral blood flow! (Important to know e.g., in a trauma patient who has a pneumothorax plus a head injury!)
2. Pressing: How to handle data that (a) are unknown because they have never been studied, or (b) are not available in a particular simulated patient.
3. Presentation: Run some simulations on HumMod.
4. Thoughts: My comment on 2. above is EXACTLY the issue of OoC when some (many) organs are missing! We need to talk to Dr. Hester and pick his brain on this question.
0. Knew: That Guyotn-Coleman provided a platform for testing physiological variables.
ReplyDelete1. Learned: What the interface looks like; level of detail. Outline of sources complexity in biomedical systems.
2. Pressing: How many variables do you need to enter for a result to be significant? Analysis of probability that HumMod's result is correct (based on inputs).
3.Presentation: Live demonstration of HumMod.
4. I agree with Frank, HumMod faces the same challenge OoC's face: compensating for unknown data.
David Wooten
ReplyDeleteSysBio13 Asgn_14A_Class_18_Article_22_2013_10_24
0. Knew: The basics of Guyton-Coleman
1. Learned: Some of the various modeling platforms for physiology
2. Pressing ?: What are the various strengths and weaknesses of the various projects they mentioned? It seemed like only the briefest of attention was given to projects other than HumMod.
3. Presentation: How to use HumMod
4. Thoughts: My impression from the abstract and intro was that this would be an article on the strengths and weakness of current state-of-the-art integrative physiology models, but it felt like everything but HumMod was given extremely surface level attention. I would be interested to know what the challenges are in linking models of individual organ systems, how HumMod got around that, and a greater level of detail on what HumMod still can't accomplish.
SysBio13 Asgn_14A_Class_18_Article_22_2013_10_24
ReplyDelete0. Knew: idea of what HumMod could do
1. Learned: the basics of other models, the benefits of top-down approach
2. Pressing: does HumMod incorporate the other model pieces or built all on its own...what are the limiting factors around incorporating the various models together
3. Presentation: a run of HumMod
4. Thoughts: so they say that top-down is best...but then they say that HumMod is a middle-out modeling approach; this seems contradicting...
also, why has there been a tendency toward reductionist physiology? this seems to be backward compared to the field...is it driven by the medical field?
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ReplyDelete0 Knew: Guyton Coleman model is important; basic motives for modeling
ReplyDelete1 Learned: a little more of what the Guyton-Coleman model is, how HumMod has branched from it
2 Pressing: The article keeps saying that these models are not a complete integrated model of human physiology... is HumMod? What are the shortcomings of HumMod? When we say Guyton-Coleman, do we really mean HumMod? Page 1059 says that "validating the total state of a model is only possible in trivial models," so how can we expect to validate a model of an entire human?
3 Presentation: Shortcomings of HumMod
4 Thoughts: I still have a lot of questions about these different models...how we use them, specifically, and what we want that they don't have. Good intro, I understand the purposes of modeling better now.
0. Knew: Guyton-Coleman compilation of equations and variables to model physiological
ReplyDelete1. Learned: history/development to HM, importance of quantitative evaluation of dynamic transition, HM formatting and advantages of some features
2. Pressing: Basic idea of top-down approach is to start from the simplest model you can come up with, keep on adding components that meet the 3-part validation, presumably increasing physiological detail/knowledge of the environment, until a model is ‘good enough’?
3. Presentation: Acceptance by scientific community as a tool, not novelty?
4. Thoughts: Overall this gave me a clearer idea of what Guyton-Coleman modelling is meant to do, they touched on necessity of addressing sex/age