This directory contains the code for hyphal growth simulation at the microscopic level as part of DTU Biobuilders project for iGEM 2018.
Mycelium growth originates from a single spore, where branching starts. Here we follow the development of the mycelium by simulating branch development during a specified time period. We focus on simulating hyphal movement through a space with homogenous substrate, hyphal tip extension and branching events and how the mycelium density/biomass changes over time.
When the simulation is completed, several plots are produced. This includes summary plots of mycelium properties, an animation of the mycelium development and a density inspection.
The main code is located in simulation_v7.R, so run that. Libraries required are:
For the fun of it, we can also simulate the letters in our team name for this year. The code for this exist in letter_simulations.R and the functions for each letter are defined in letter_funcs.R.
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