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CM Tutorial 2
Open the Colab notebook here.
View the generated script here.
In the Colab notebook, press the start button on cell one to setup the environment.
Download the BBa_02.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 simulates the repression of RFP by TetR, which is repressed by the small molecule aTc. The non-diffusible external chemical aTc is set at an initial concentration across the simulation which does not change. The value selected for this concentration must be reasonable to see the expected results, as otherwise either RFP or TetR will grow much too large without the necessary repression. Each cell's color is calculated using its concentration of RFP.