Panel 1 - Simulation Parameters

Before simulating a model, five simulation parameters need to be defined. The simulation method allows the user to select either stochastic simulation or deterministic simulation (ODEs) in the drop-down menu. Right below the simulation method, the user can set the simulation time either in seconds or in number of reaction events. Note that if the activity of the system drops to zero (i.e., no more rules can be applied), then the simulation may stop prematurely.

The user can choose how many data points are recorded in the simulation results. The indicated number of time points are sampled evenly from the full expected simulation time, so if the simulation ends prematurely then fewer than expected time points will be returned. The simulation graph displays about 400 points but if the user downloads the CSV file in the Actions menu (Export Simulation Results to CSV), it will show the defined number of data points.

For stochastic simulations only, the number of times or iterations a simulation should run needs to be defined. Having more than one iteration allows the user to compare the noise in the system. The maximum number of iterations for a simulation is four. The last parameter to define is the reaction volume which is expressed in liters. See Reaction Volume for more details.

Panel 2 - Observables

Observables are basically what the user wants to track during the simulation. Observables are much like the patterns used in rules - any given observable can match with many different possible complexes that may be formed during a simulation. Thus observables act as general descriptions of proteins or complexes that are of interest. Generally, observables can be used to track experimentally relevant (indistinguishable) species and complexes.

Observables can be added by clicking on the "+ Add" button and the observables editor (below) will appear. The user can drag the agent(s) they want to track into the right hand side of the editor. See Complex Editing for more details about drawing bonds. The user can choose sites on the selected agent using the "Pick Sites" button. Sites are added with their initial state, which can be changed by selecting the state and clicking on the "edit" button. A window will pop up, showing all the states defined for the site. The user can name the observable but it is optional. After saving the observables, the user can edit them using the "Edit" button and delete them using the (x) button.

Panel 3 - Snapshots

Snapshots capture the complete state of the system, including all existing complexes and their abundances. The final state is a snapshot of the system at the termination of the simulation. This feature is only relevant for stochastic simulations. The user simply has to check the box if they want to see snapshots of the final state of the system. After running a simulation, a Snapshot tab will automatically appear so the user can see the final abundances of all existing complexes.The user can also download a CSV file of the snapshots using the Actions menu (Export Snapshots to CSV).

Panel 4 - Rule Activity

In addition to solution observables, the user can select rules to track during the simulation. The rule activity is not the actual execution of the rules themselves, but rather the propensity of the rule to act at any point in time. Thus rule activities are equivalent to tracking observables for the reactants in the rule, and taking the product of the amounts of these observables and the rate constant for the rule. The user can add and edit rule observables via the rule picker.

Panel 5 - Perturbation Events

Perturbation events are a means to change the rate constants of individual rules in the middle of a dynamic simulation.  Each perturbation is applied when a particular trigger condition is met. Perturbations can be triggered at a particular time in the simulation, or when an observable increases or decreases past some threshold. Learn more about Perturbations.

Panel 6 - Hide Editor and Run Buttons

The Hide Editor button hides the entire Simulation Settings part of the simulation panel.  The Run button executes the simulation as defined by the Simulation Settings, Rules, and Initial Conditions.