Eye Development Model

Introduction:

Eye Development Model (EDM) is a python application used to model and simulate the growth and development of eyes given different parameters. The model is based mainly on what is known about the development of D. melanogaster eyes. The user can observe in 2D what causes differentiation between different eye types by changing individual parameters of the cells. The application is designed to also allow the user to define their own events to occur to on the epithelium of the eye.

Starting EDM

Quick version:

1. Download Python version 3.7 or greater

2. Install PyCharm. If you opt to not use PyCharm, you will need to install dependencies with something like pip.:

   • pyopengl - version 3.1.0
   • moderngl - version 5.5.3
   • numpy - version 1.17.2
   • pyrr - version 0.10.3
   • wxPython - version 4.0.6

   PyCharm uses requirements.txt to automatically get the needed packages.

3. Get EDM with git clone. Or download a zip of Eye Development Model

   git clone https://github.com/buschbeck-lab/EyeDevelopmentModel.git

4. Open the project in PyCharm

5. Run main.py

For a more detailed description of how to get up and running see this user guide.

General Use

Epithelium Generation

An Epithelium can be generated or loaded from the Epithelium Generation tab in the top left. After an epithelium is generated it can be saved to be loaded later or sent to someone else to load.

Simulation Overview

The simulation Overview tab will let you start, stop, and pause a simulation as well as change any of the simulation's parameters, or any of the parameters used for cell specialization.

Simulation

The Simulation tab will only let you start, pause, and stop the simulation, but it provides a better view.

Reporting Bugs

Please report any and all bugs to the GitHub Issue Tracker