CM Tutorial 4
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_04.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 YES-gate, in which GFP or RFP is repressed by LacI, which is repressed by the non-diffusible chemical IPTG. The initial supply of IPTG is set across the entire grid at the beginning of the script. This causes GFP or RFP expression to turn off when there are enough cells producing LacI, as IPTG can no longer repress enough LacI to keep GFP or RFP expression on. Note that the example simulation uses RFP while the example script uses GFP.