Update 03_fba.md

jcwang587 · Dec 15, 2024 · 4ecdecf · 4ecdecf
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 Methodology for flux balance analysis.
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-This is a very simple example for an FBA study, as shown in the Figure 5 (a), we will call the inside of the cell intracellular and outside cell as extracellular. The idea of picture figure (a) is that the cell consume something from the b1 side and b1 is the rate of consumption. Then it takes across the membrane that is called uptake, and once it is inside the cell that will called A . And then you see there is a series of reactions between these metabolites A B and C. And these reactions A to B and C to B are irreversible, and the one between A and C is reversible reaction.
+This is a very simple example for an FBA study, as shown in the Figure 5 (a), this is not a cell but it depicts a make-believe cell. we call the inside of the cell intracellular and outside cell as extracellular. The idea of picture figure (a) is that the cell consume something from the b1 side and b1 is the rate of consumption. Then it takes across the membrane that is called uptake, and once it is inside the cell that will called A . And then you see there is a series of reactions between these metabolites A B and C. And these reactions A to B and C to B are irreversible, and the one between A and C is reversible reaction.
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+And then what it depicts is that the cell can take this metabolite B and secrete it. Okay, meaning you can take this and move it outside the cell, and it can do the same thing with C. Okay, those are called secretions. So this is called uptake, and these two things are called secretions. And so this is just kinetics, basically. Okay, so this is nothing but, well, it's even simpler, it's just like mass balances. So what you do in a real cell, okay, there's going to be several hundred of these things. And there's going to be, you know, maybe a hundred of these things. And inside here, there won't be three metabolites, there'll be about, I think in our model, there's about 4,000.