The wet-lab model was written in BioNetGen Language, a rule-based modeling language that is useful for generating differential equations from a description of how various biological components interact with one another. The wet-lab model was constructed from both data found in the literature and data from the wet-lab itself. This allows the model to run various simulations of the experiment under different conditions in order to find the most optimal conditions for running the experiment. Also if the wet-lab run of the experiment is not producing any measurable results, the model can be used to identify exactly which component of the wet-lab experiment could be the problem.
The Outline
The model captures a total of 17 different interactions.
1. The rate at which mRNA T7-Intein is transcribed.
2. The rate at which mRNA T7-Intein is degraded.
3. The rate at which T7-Intein is translated.
4. The rate at which T7-Intein is degraded.
5. The rate at which T7 polymerase is degraded.
6. The rate at which estrogen enters the cell.
7. The rate at which estrogen leaves the cell.
8. The rate at which estrogen binds to the intein.
9. The rate at which estrogen disassociates from the intein.
10. The rate at which the intein is spliced out and T7 is formed.
11. The rate at which T7 binds to the promoter of plasmid 2.
12. The rate at which mRNA RFP is transcribed.
13. The rate at which mRNA RFP is degraded.
14. The rate at which RFP is translated.
15. The rate at which RFP is degraded.
16. The rate at which YFP is translated.
17. The rate at which YFP is degraded.
To run the model simply open the latest version of Rulebender, go to the simulation tab, provide the file path for the file you wish to run, and hit run.
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