Quantitative App

DNA binding to TALEs

The target DNA's are colored red, non-target DNA is green, TALEs are black and after binding (i.e. saturation) they turn blue. The sliders under "global settings"€ are parameters needed before the simulation runs. Given that a simulation can take 30 seconds to complete, they should not be changed frequently as it will take longer to show the results. The sliders under "€œdisplay settings"€ are parameters needed after the simulation runs. Their responses are much faster and are best played by clicking on the plus sign to the right and hit "€œPlay". If you only see a grey box, you may need to install the Mathematica CDF Player. The download link can be found here. Otherwise, the data from our model, as well as images of the app we designed, can be found on the quantitative modelling page.

Enzyme kinetics of horseradish peroxidase

The sliders above the plot are parameters you can adjust to this kinetic model of horseradish peroxidase. By moving to the right you increase the corresponding parameter and immediately you should see the response on the plot, colored blue. The red line is plotted at the initial conditions when you run the model. It is included so that by comparing against it you see the effect of the change in the parameters. For a quick feel of the model, click on the auto-run button on the upper-right corner.

Enzyme kinetics of beta-galactosidase

The sliders above the plot are parameters you can adjust to this kinetic model of horseradish peroxidase. By moving to the right you increase the corresponding parameter and immediately you should see the response on the plot, colored blue. The red line is plotted at the initial conditions when you run the model. It is included so that by comparing against it you see the effect of the change in the parameters. For a quick feel of the model, click on the auto-run button on the upper-right corner.

Frequently Asked Questions

1. Can I see your code?

Sure! Here are DNA binding to TALEs agent based model, horseradish peroxidase kinetic model, and beta-galactosidase kinetic model.

2. I see a block of text with red background. What should I do?

Don't worry, everything is under control. For the DNA binding to TALEs agent based model, wait for at least 30 seconds. If the problem persists, reset the current time to 1. For the kinetic models, use the plus/minus sign to change the parameters, or simply hit auto-run on the upper-right corner.