CM Tutorial 6
Open the Colab notebook here.
View the generated script here.
Generated simulation:
In the Colab notebook, press the start button on cell one to setup the environment.
Download the BBa_I5200.xml from here and upload it into the second cell. Then press the start button on cell three to convert it into a json.
Press the start button on cell four and edit the parameters to fine tune simulations. To recreate the example, leave values at defaults. Click the Save Parameters button and then the Generate CellModeller Script button. Copy the output.
Open WebCM and create a new simulation. Click the Edit Source button and paste the generated script. Click the Save Source button. Then, in the simulation window, click the Restart button to run the simulation. If no traveling waves are appearing, make sure the inital concentrations of proteins are not all the same, and adjust the production and degradation rates or the hill coefficient.
This script simulates an Elowitz repressilator, in which TetR represses cI, which represses LacI, which repressses TetR and GFP. This creates an oscillator with a traveling wave of GFP expression, which looks like a wave of black moving from the edge of the colony to the center. This is caused by the different growth rates of cells in different locations, which affects the growth rate of proteins within the cells. Due to mechanical forces, cells closer to the edge will be in a slightly different oscillation state than cells closer to the center, which synchronizes the colony and allows for traveling waves.