Managing SimBiology Projects and Libraries from the Desktop

Desktop Management and Navigation Aids

SimBiology Desktop With an Open Project and a Model Selected

Use the following to manage and navigate models and data in a project and to manage libraries:

  • Toolstrip — Displays the Home tab and other context-sensitive tabs.

  • Home tab — Use to open and manage projects, including adding models, tasks, and data to a project.

  • button — Use to select a project, model, task, or data to view and edit in the desktop window. Use to navigate between models, tasks, and data. Use to select and view a library, and to navigate between libraries.

  • Additional tools button — Use to select actions appropriate for the item (project, model, data, or library) selected and displayed in the desktop.

Working with Models in the Desktop

Opening, Creating, and Editing Models

After selecting a model, you can do the following from the Model tab or desktop window:

  • Open a model page from the Model tab using the Open button.

  • Create and edit the quantities and expressions that define the model.

  • Create and edit modifiers (variants and doses) for the model.

Using a Model-Centric Workflow

If you want to refine a model, select the model from the address bar, then perform iterative edits on the model. Without leaving the model, you can run multiple tasks and view results to help guide you with your model edits.

Working with Analysis Tasks in the Desktop

Creating and Editing Analysis Tasks

After selecting an analysis task (for example, calculate sensitivities or run scan), you can do the following from the Task Editor window.

  • Select a model to run the analysis on, optionally select a variant or dose, and then define the model's simulation settings.

  • Define the settings of the analysis.

  • Select the plots to generate when the analysis completes.

  • Adjust quantities and doses using the Explorer Tools.

  • Run the analysis.

For more information on available analysis tasks, see Simulation and Analysis.

Using a Task-Centric Workflow

You can perform iterative runs and edits on the task to refine an analysis task. Without leaving the task, select different models to run the task on or adjust quantities or doses using the Explorer tools. For example, select different models for a parameter fit task to find the model that best fits the data.

Creating Plots of Analyses

To visualize data from analyses, you can choose from a list of built-in plot types. You can also create your own plot types that extend or customize the built-in plot types. Create a custom plot type in the Plot Types library. For more information, see What Are SimBiology Libraries? and Using Libraries from the Desktop.

Creating Custom Analysis Tasks

You can create a custom analysis task from scratch or use the code of an existing task by adding a Create custom analysis task.

Working with Data in the Desktop

Importing and Generating Data

There are two types of data to manage in the desktop:

  • Imported data — Data that you import from external sources to use for an analysis (such as parameter fitting) or to use to compare to results from a simulation or analysis.

  • Task data — Data generated from analysis tasks.

After you import or generate data, select the data from the address bar to view, plot, and manipulate it as described in Working with Imported Data and Working with Task Data.

Working with Imported Data

You can do the following with data that you import:

  • View raw data — When viewing imported raw data, you can specify the units for the column headers.

  • Plot data — Select from a list of built-in and user-defined plot types.

  • Exclude data — Exclude rows of data that meet or don't meet certain criteria, using column headers and relational operators. For example, you can exclude outliers in a data set, such as rows containing a DOSE value > 20.

  • Add derived data — Create additional columns of data that you derive from the existing columns of data using expressions and relational operators. For example, you can convert a column header to different units, or create a ratio of two columns of data.

  • View data statistics — View statistics, such as minimum, maximum, mean, and time of maximum.

Working with Task Data

You can do the following with data generated from an analysis task:

  • Save data — When you generate data from an analysis task, you can save the data to prevent it from being overwritten by subsequent analysis tasks. Saved data includes the task analysis settings used to create it.

  • View raw data — Inspect the raw data generated by a simulation or analysis.

  • Plot data — Select from a list of built-in and user-defined plot types. You can plot data without having to rerun the analysis task.

  • Export data — Export analysis task data to a file or a variable in the MATLAB® Workspace.

Importing and Exporting Models, Tasks, and Data from the Desktop

Models

You can import models from any of the following:

  • sbproj file

  • SBML (file or URL)

  • MATLAB Workspace variable

You can export models to either of the following:

  • SBML file

  • MATLAB Workspace variable

For more information on how SimBiology® supports SBML, see SBML Support.

Tasks

You can save a task as code in a MATLAB file.

Data

You can import data from any of the following:

  • sbproj file

  • Microsoft® Excel® file

  • txt or CSV file

  • MAT-file

  • MATLAB Workspace variable

Select Export Data from the Actions button to export data to a MATLAB Workspace variable, MAT file, or Microsoft Excel file (Windows® only).

Searching a Project from the Desktop

To do a simple search of a project, use the button above the toolstrip.

Alternately, create search criteria to find specific components in the models in a project by adding a Search model task. After editing or loading a project, you must execute a search to have up-to-date results. Like other tasks, a search model task is saved with the project.

Generating a Project Report from the Desktop

You can generate reports (HTML) with model-specific information, such as analysis task results, imported data, and searches, by adding a Generate report task. Like other tasks, a report task is saved with the project.

Using Libraries from the Desktop

After selecting a library (using the button or the address bar), you can:

  • Add user-defined components to a library — You can add, modify, and delete user-defined components in a library, but you cannot modify or delete built-in components in a library.

  • Export and import libraries — Export user-defined components from a library to an sblib file, which another SimBiology user can import.

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