A noob question, since the original article doesn't go into details - what is exactly being simulated here? I was under the impression that we can't even reliably do a single protein folding due to the sheer complexity of the task. So how do we simulate the zillions that are bouncing around in a single cell? And if we don't simulate it at that level, how are we confident that it is correct?
moralestapia|8 months ago
Most of them are built around one specific, measurable, phenotype that they want to reproduce, like estimate metabolite input/output over time.
Some others attempt to model the behavior of these cells when interacting with others, like in a colony or tissue. This is quite important because most of the phenomena that enables development, healing, regeneration, etc ... are emergent processes that only make sense when you study the whole tissue. One concrete thing you can measure/simulate here is "if I drop this hormone here, where is it going to be at time X and at what concentration" [1], which is super useful to do in silico because measuring that in real tissue, without or even with markers, is much more complicated, expensive and time consuming.
1: I wrote one of the first models that was able to do this in realistic plant tissue. Realistic here means, bounded by the chemical/physical constraints found in real plants and using a structural scaffold that resembles them as well.
andoando|8 months ago