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Sal@mander.xyz

Gene regulatory network - Clock and Flip-flop (diode.zone)

submitted 2 years ago by sixfold@lemmy.sdf.org to c/biology@mander.xyz

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I'm working on a program to edit and simulate gene regulatory networks using recurrent neural networks as a model. Here's a demo.

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[–] sixfold@lemmy.sdf.org 1 points 2 years ago* (last edited 2 years ago)

Well, it is technically differential equations, but with weighted inputs like a NN. Here's the equations

for each node (gene/morphogen) i. zi is the concentration of morphogen i, zj is that of j. f(x) is the sigmoid function, k1 is the maximum rate of expression, k2 is the degradation rate, b is the bias. wij is the weight for an edge from j to i.

This is just written in python, so the network is defined by a matrix with each number representing the weight between two of the edges. I ignore the edge if it's weight is zero.

What are the standard symbols for genetic circuits?

edit: sorry it's impossible to see the equations if you have a black background.