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.
Wednesday, February 15, 2012
Asgn_10A_Class_16_Article_12_2012_02_17
Article 12: Chen KC, Calzone L, Csikasz-Nagy A, et al.,Integrative analysis of cell cycle control in budding yeast, MOLECULAR BIOLOGY OF THE CELL, 15(8) 3841-3862 (2004). Review this to get a general idea of the complexity of the model that Tyson has assembled to explain the cell cycle. Do not attempt to master the details. Post a PCRC.
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Will Matloff
ReplyDelete10A/Tyson Cell Cycle Model
0. Knew: Basics of chemical modeling.
1. Learned: A cell cycle model of yeast was created using differential equations. The model could predict the changes in the cell cycle of yeast mutants.
2. Pressing?: Have these types of models been successfully used to predict how a biological system would react to new perturbations?
3. Presentation: Cell modeling.
4. Thoughts: It is interesting how a lot of the process of model creation, as they mention, is trial and error.
Zach Eagleton
ReplyDelete10A/Tyson Cell Cycle Model
0 Knew: Basic cell cycle dynamics
1 Learned: Tested 131 mutant strains and 120 worked well with the model. That the cell cycle of yeast was reasonably well modeled using differential equations.
2 Pressing ?: How has this model been improved since 2004? Has it become more accurate.
3 Presentation:JigCell
4 Thoughts: Thought the paper was very technical and unless you are doing the reading really in depth and looking at all the Diffeqs that are listed then the jist of it is that he has come up with a mathematical model that pretty well describes the yeast cell cycle and its response to mutants.
Erica Curtis
Delete10A/Tyson Cell Model
0. Knew - Basics of how to model signaling in cell cycles.
1. Learned - How to turn a mechanistic hypothesis into a mathematical model.
2. Pressing Question - How could Tyson's model be improved by "closing the loop"?
3. Presentation - How to Avoid Trial and Error Experimentation in Systems Biology
4. Thoughts - Despite being highly technical, the paper was able to impress the general concepts behind cell modeling and the complexity of it all.
Ayeeshik Kole
ReplyDelete10A/Tyson Cell Cycle Model
0. Knew: General understanding of the budding yeast cell cycle.
1. Learned: By describing gene and protein interactions in terms of differential equations, one can build an accurate model that can predict cell cycle behavior in quantitative detail.
2. Pressing?: How long does it take to run computer simulations? Is it very resource-intensive?
3. Presentation: Status update on "Problem-Solving Environments"
4. Thoughts: Very thorough paper. Table of parameters and technical details were hard to follow though.