General Workflow

The SimBiology® desktop is a user interface with a set of integrated tools that are designed to facilitate building, simulating, and analyzing models of dynamic systems. It provides an interactive interface to build models and perform model analyses such as simulation, sensitivity calculation, and parameter estimation. It lets you save your modeling work as a SimBiology project that contains models, experimental data, model analysis tasks, and task results.

A SimBiology model is a set of quantities and mathematical expressions that represent a dynamic system. Expressions describe the mathematical relationships among quantities. For details about SimBiology models, see What is a Model?.

The desktop lets you build such a dynamic model interactively. One approach is connecting graphical blocks that represent modeling elements such as quantities and expressions. Alternatively, you can build a model by entering expressions as strings such as A –> B, where A and B are quantities participating in a transformation process.

Once you have a model, you can perform analyses on it. For instance, you can simulate the model to see its dynamic behavior over a time course or explore biological variability by simulating alternate scenarios. You can also perform parameter scans and sensitivity analysis to investigate the influence of model parameters and initial conditions on model behavior. To help you perform these analyses, the desktop provides built-in scripts with a user interface called tasks.

You can import time-course data to the desktop. It provides tools for filtering and visualizing the data. Once imported, you can use the data to estimate model parameters or compare to simulation results.

As you build and analyze models, you can use built-in components from libraries. For instance, the units library provides the unit functionality and has a collection of predefined units that you can use in your model. To help you build models graphically, the desktop provides the blocks library with blocks representing different modeling elements. Custom elements can be added to any of these libraries. For details, see Libraries.

As you work on models and analyses, the desktop continuously checks if there are any errors or warnings and indicates them using message indicators. You can hover over each indicator to see the corresponding warning or error message.

Preferences let you customize model building and display settings, task settings, and search options.

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