CM Tutorial 3
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_03.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.
This script models the Lux-quorum sensing circuit. Using diffusible external chemicals to gate production of protein compounds, the expression of GFP is gated until there are enough cells in the colony that the production of the GFP-activating compound outpaces the loss to diffusion into the grid. Once enough cells have divided, the middle of the colony begins expressing GFP, which causes the cells to turn green.