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Python code to control my physical model of an Epigenetic Landscape.
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README.md
lp.py
main.py
sensor_code.ino
simulator.py

README.md

Epigenetic_Landscape

Python code to control my physical model of an Epigenetic Landscape (plus the arduino code used to send the IR sensor data over serial). To see more about this project, check it out here: http://brianbartz.com/pages/selected/epigenetic_landscape.html . Using a Raspberry Pi, two Arduinos, and a bunch of servos and IR reflectance sensors, this project aimed to physically model an epigenetic landscape, illustrating cell fate decisions using C.H. Waddington's metaphor of balls rolling down hills into attractor states determined by genetic regulatory networks. This code controlled the physical model by moving a grid of motors, causing tension cables to pull a membrane into a programmed shape . The main script handles the motors and sensors which encode the motor positions. The simulator script was written by David Gibbs at the Institute for Systems Biology. It simulates a timecourse for a simple genetic regulatory network motif (described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098230/), outputting a normalized probability grid of protein concentrations once the network has reached a stable state. The lp script handles user interaction with the simulation by allowing individuals to input initial parameters into the network model.

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