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.
Juan Gnecco
ReplyDeleteAsgn 6B conrol
Knew: The intrinsic ability of a cell to regulate its needs by feedback and feed foward mechanisms and the complexity that creates in trying to model it. It is a highly dynamic and highly regulated system. Actuators vs sensors.
Learned: The capability and pursuit to open the loop and control the the system. That the voltage clamp is a classical example of the control of cell through open loop.
Pressing: Should we not focus investigation on finding the endogenous biological sensors as was done for voltage gated ion channels?
Presentation: About the dynamic control of the cell and how we can bioengieer ways to control and study this system
Thoughts: This is clearly a bionegineering problem in order to create devices. What is the control mechanisms for inflammation (how does it know to stop)? The glucose clamp seems interesting.
Juan Gnecco
ReplyDeleteAsgn 6B conrol
Knew: The intrinsic ability of a cell to regulate its needs by feedback and feed foward mechanisms and the complexity that creates in trying to model it. It is a highly dynamic and highly regulated system. Actuators vs sensors.
Learned: The capability and pursuit to open the loop and control the the system. That the voltage clamp is a classical example of the control of cell through open loop.
Pressing: Should we not focus investigation on finding the endogenous biological sensors as was done for voltage gated ion channels?
Presentation: About the dynamic control of the cell and how we can bioengieer ways to control and study this system
Thoughts: This is clearly a bionegineering problem in order to create devices. What is the control mechanisms for inflammation (how does it know to stop)? The glucose clamp seems interesting.
Cameron Togrye
ReplyDeleteAsgn_6B / Examples of Control
0. Knew: The fundamentals of positive and negative feed back, and some biological examples of these control loops in action.
1. Learned: We have developed tools to "open the loop" so to speak, and thereby are given the opportunity to play with the controls on previously biologically autonomous scenarios such as action potential propagation.
2. Pressing: On the question of what is life and whether it can be defined by control, I would forward a couple of examples which appear to exhibit little to no control mechanisms, but are currently debated forms of life; prions, viruses, cancer cells perhaps? Also, I'm not entirely clear on the difference between closed and open loops.
3. Presentation: Other examples of control mechanisms tooled towards biological phenomena
4. Thoughts: What is the benchmark for control? When can we determine the influence of disturbances in the control scheme have been properly mitigated?
Kate Jones
ReplyDeleteAssignment 6B Control
0. Knew: I knew the basics of control diagrams, mapping control mechanisms, negative and positive feedback loops, Hodgkin Huxley model of membrane potential and current across membranes, and the voltage clamp experiments.
1. Learned: Opening the loop allows you to analyze the feedback loop and better understand the control mechanism. I also learned the definitions of observable, controllable, detectable, and stabilizable as applied to biological control systems.
2. Pressing ?: Is the goal in understanding control mechanisms in biology to better understand how cells and tissues interact so we can create better models or to ultimately control them?
3. Presentation: I'd appreciate a little clarification of the control stability graphs. Also, I'd be interested in learning more about Kao neuromuscular/humeral feedback on slide 13.
4. Thoughts: I think that the question of is life control is an interesting topic. We may think of something as seemingly random when in actuality it is controlled by some mechanism we are unaware of and may never be.
Chuck Herring
ReplyDeleteAsgn 6B conrol
Knew: The basics about control systems.
Learned: The technical definitions of controllable, observable, and stabilizable.
Pressing: Can you monitor at single cell resolution (and lower) without disturbing the system? (I believe it can be, with proper controls)
Presentation: About control of cell biology as a means to greater understanding.
Thoughts: How does scale to the tissue level? Cell heterogeneity contributes to the homogeneity of tissues, I fell like controlling single cells to monitor tissue level outputs would be a significant challenge.
Tim Lee
ReplyDeleteAsgn_6B
0. Knew: Basics of control and feedback loops.
1. Learned: Examples of applications of control and feedback loops such as Kao neuromuscular/humeral feedback and Hodgkin-Huxley. Definitions of controllable, observable, stabilizable, and detectable.
2. Pressing: Are there more examples of closed loop feedback and what kind of insight that can give us? I still don't quite know what closed loop means.
3. Presentation: Control and feedback in biology and the insight it can give us.
4. Thoughts: I really like how in depth the presentation went on what is controllable and what that entails. Don't really know how to answer the what is life question.
Nate Braman
ReplyDeleteAsgn_6B
0. Knew: Control is an important component of biological systems, and these mechanisms can be modeled quantitatively.
1. Learned: Specific examples of biological control systems. What a control diagram for a biological system looks like, generally.
2. Pressing ?: What are the limits of depicting a control system with these diagrams? Would this still be a useful tool for the visualization of systems on the level of complexity of an RTA device?
3. Presentation: Presentation highlighting some examples of biological controls and the models which be used to understand them.
4. Thoughts: I agree that this should be part of the Vanderbilt BME curriculum. I can understand these diagrams, but don’t think I could intuitively construct one.
Cami Johnson
ReplyDeleteAssignment 6B: Examples of Control
0. Knew: The basic concepts of control. The advantages of learning how to open biological feedback loops and control them.
1. Learned: Different examples of control in biological systems. Different ways we have opened the feedback loop and taken control. What defines a system as controllable, observable, stabilizable, or detectable.
2. Pressing ?: In terms of the question on the slide "what are we optimizing," are we really optimizing anything? Aren't we more just trying to hijack the control system in a sense, in order to be able to manipulate it and better understand it?
3. Presentation: examples of ways researchers have been able to open the feedback loop and control it
4. Thoughts: The question "is life control?" really made me think about how control is everywhere. In biology, in behavior, in nature. It's really interesting how you can find feedback in so many situations.
Mark Vander Roest
ReplyDeleteAssignment 6B
0. Knew: Basics of linear control and how they can be applied to cellular processes, potential benefits of achieving higher levels of control in cells.
1. Learned: The definitions of controllable, observable, stabilizable and detectable in terms of cellular functions, various examples of control, a new mindset for different cellular processes like the HH model of action potentials.
2. Pressing ?: What would a black box model of cellular control on a systems bio level look like? We can model specific ions flowing through specific ion channels, but isn't that a little too nitty gritty to be of practical use in systems bio practices?
3. Presentation: Various examples and definitions of control at the cellular level.
4. Thoughts: These slides broke down linear control in a very approachable way for someone who has no background in it.
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ReplyDeleteJPW