CM Tutorial 5
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_05.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 a cascading line of repression beginning with the external chemical aTc and ending with GFP. The aTc represses TetR, which represses cI, which represses LacI, which finally represses GFP. The higher the initial aTc concentration, the longer it takes for GFP expression to turn off, as it will take longer for enough TetR to accumulate.