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. Understood the basics of the Guyton-Coleman and modeling from previous readings and discussion.
ReplyDelete1. Seeing the part of the C++ code and the GUIs was useful in terms of understanding how someone interprets / reads the output information.
2. What I envision as a pressing issue within the Guyton-Coleman model and code presented is the flexibility to represent a more detailed issue. For example if some has sickle cell anemia how do you model that within the model beyond the oxygen level. I believe that there would be great complications in terms of pressure, clots, and delivery to distant tissues that is being missed with the broad manipulation settings that currently exist.
3. Guyton-Coleman 101
4. I found this article useful in conjunction with the previous article in terms of understanding what is going on.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_14B_Class_18_Article_23_2013_10_24
0. Knew: Prior versions of Guyton-Coleman.
1. Learned: Simulation models what happens over time ... e.g., fast vs. slow deterioration of cardiac function.
2. Pressing: How to integrate bidirectional communication with this and OoC.
3. Presentation: Demo of some of the scenarios (or at least some from Guyton-Coleman prior version).
4. Thoughts: We need to get seriously involved with this project and get them involved in ours!
0. Knew: First HumMod paper.
ReplyDelete1. Learned: More about user interface and customizability. Multilevel mathematical models elucidate physiological trends not seen readily by direct experimentation.
2. Pressing: With what resolution can HumMod determine the mechanism of heart failure? Many factors (ion channel mutations, ion channel transport protein mutation, scarred tissue, etc.) affect left ventricular contractility.
3. Presentation: Heart failure in HumMod.
4. Thoughts: HumMod does a good job integrating organ systems, a weakness of the OoC projects. The OoC projects can generate data with higher resolution that HumMod. Perhaps HumMod can act as the software (big brain) for Athena.
David Wooten
ReplyDeleteSysBio13 Asgn_14B_Class_18_Article_23_2013_10_24
0. Knew: Basics of G-C
1. Learned: HumMod is a modern extension of the original Guyton-Coleman, with XML specification of models.
2. Pressing ?: What kind of interfaces does HumMod have for batch processing, and (more importantly) exporting data for external analysis?
3. Presentation: Data analysis in HumMod
4. Thoughts: I think that the models in HumMod will be very helpful for OoC design, but (without having played with it much) it's hard to imagine that their GUI is designed for the vast amount of data processing we need to do. I'm looking forward to the meeting with Dr. Hester!
SysBio13 Asgn_14B_Class_18_Article_23_2013_10_24
ReplyDelete0. Knew: what had been mention in class about the abilities of HumMod
1. Learned: the interface, how the user can change the simulation and monitor outputs
2. Pressing: Do you set all of the variables for every simulation/have initial conditions or is it still pieces that you are running, like the cardiac portion? They have a good interface for looking at a few variables at a time, but how are you supposed to make sure everything is working properly when you have to monitor so many variables...do they have a "patient in stress" kind of error message or something to tell the user something is amiss?
3. Presentation: looking forward to having Dr. Hester
4. Thoughts: was thinking along the same lines as Christopher...having the HumMod as the brain...great point of discussion that should be brought up in class
0 Knew: Basics of HumMod as discussed in other paper
ReplyDelete1 Learned: how HumMod can be set up to run simulations, the ability to expand upon it using the XML
2 Pressing: p. 2 discussed modeling chronic renal failure. how is this accomplished? or any disease in general? later they discuss setting initial values... would these designate a disease state? if so, how would these values change once simulation began? How can this be integrated with OoC?
3 Presentation: Demonstration of HumMod
4 Thoughts: got a little bogged down in the technical/coding explanations but I understand the overall concept a lot better. still wondering... what can this NOT tell us? why do we need OoC's/how do we use the two together?
0. Knew: HM from previous paper, modelling via Guyton-coleman
ReplyDelete1. Learned: facility of manipulating variables and equations, deeper detail of HM’s user interface, general course of action is a hypothesis is inferred and an experiment is designed, examples of system response illustrated HM at work, progressive perturbations
2. Pressing: Interface between in vitro OoC experiments/data collection vs in silico simulations/hypothesis probing? Third-party compiler of HM progress?
3. Presentation: in-house demonstration
4. Thoughts: Notion of studying system mechanics by applying a perturbation came up again, also I’m sure that some important nuance was explained by the examples that got lost in the middle of all the details