Task Editor

Each task in the SimBiology desktop opens within the task editor, where you can edit the task settings, explore model parameters, and visualize live simulation results. If there are multiple tasks, each task opens in its own tab within the editor. The editor is composed of the Task, Explorer Tools, and Live Plots. You can display each of them by selecting the appropriate toggle button in the Editor tab. The tab also contains other options to add new tasks, view equivalent MATLAB code of the task, create standalone applications, and run the task.

The Task gives you a graphical way to define what is executed when you run a task. Suppose you have a variant that has an alternate set of parameter values for a cancer patient and you want to simulate the model using those values. You can specify the variant in the Variants to Apply section of a simulation task and run it. For more details about each section of a task, you can hover over the information icon to see its context-sensitive help. As you configure the task, the desktop checks for any errors or warnings and flags them using message indicators. For details, see Configuring Tasks.

The Explorer Tools let you explore parameter values, initial conditions, and dose schedules with sliders. These interactive tools let you quickly iterate through values without modifying the base model. For instance, you can vary a model parameter value and find out an initial value that generates simulation results closer to experimental observations. Then you can use the value as an initial estimate when you perform parameter estimation. You can also calculate statistics on simulation results using mathematical expressions to get better insight into the results. For instance, if you want to calculate an AUC (area under curve) of the concentration-time curve of a drug, you can write an expression such as trapz(drug).

The Live Plots show the live simulation results as the task is running. You can also add experimental data points to compare with simulation results or define a mathematical expression to plot by right-clicking the live plot.

The tools for working with Live Plots and Explorer Tools are also listed in the Explorer tab. For instance, you can select which quantities or doses to explore, overlay simulation results in the live plot, or add new plots.

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