Simulator

Wiki-integrated simulator

A simulation graph is worth a thousand words. But an integrated, user-controllable online simulator is worth a million.

Explanation

In order to make our models easier to understand, we have created an on-line simulator fully integrated in the iGEM wiki system. This simulator uses the aforementioned HSIM rules and implements one of the HSIM algorithms that can be summed up as the following series of steps :

1. Randomly reorder the reaction list
2. Compute the number of reactions to execute : *R*. R is a rational number proportional to the concentrations, the reaction probability, and a constant factor α.
3. Execute the reaction integer part of R times
4. Execute it one more time with the probability decimal part of R

See the reference article for more details.

This self-contained simulator is written in standard HTML5 and is therefore compatible with the iGEM 2013 rules which forbid the embedding of plug-ins and external data.

How to control the simulator

Our wiki-based simulator in action

The simulator is easy to use. The graph represents the live quantities of the different molecules as a function of time. The line color for each molecule is shown just below the graph. The controllable quantities involved in the simulation also appear under the graph. Finally, there are two control buttons : START and RESET.

In order to launch a simulation, you can press START. To pause it, click on this same button again. Another click will resume the simulation. While the simulation is paused, you can modify the controllable quantities. If you want to reset the simulation to its initial state and default molecule quantities, just click on the RESET button.

How to include this simulator in your wiki

This simulator is designed to be simple to use. You can embed your own by following these steps :

• First upload a copy of our script available here : HTML5 simulator code