Explore the Edit Menu

The Edit Menu in Certara's Quantitative Systems Pharmacology (QSP) software enhances user efficiency by offering essential functions like undo/redo, cut, copy, and paste, as well as data sorting and searching options. Users can insert or delete rows and columns, freeze panes, and locate specific cells by their coordinates. The menu also allows direct editing of worksheets in Excel and access to the Preferences dialog, ensuring a customizable experience. This set of tools simplifies data management, aiding researchers in effectively analyzing complex datasets.

The 'Undo' option reverses the last undoable command. Use the keyboard shortcut 'Ctrl + Z' for quick access. Any action that modifies the workspace qualifies as an undoable command. For example, editing a species name is undoable, while changing the zoom level is not.

The undo queue is cleared in the following scenarios:

Click the 'Redo' option to reapply the last undone command, if available.

If the 'Selection Mode' is set to 'Entities', clicking 'Select All' will select all entities. If the 'Selection Mode' is set to 'Edges', clicking 'Select All' will select all edges.

Click the 'Cut' option to copy and remove the selected module or entity from the canvas.

Click the 'Copy' option to duplicate the selected module or entity from the canvas.

Click the 'Paste' option to insert the copied module or entity onto the canvas.

Click the 'Paste Visual Clone' option to paste the Visual Clone copied from the canvas. The keyboard shortcut is 'Ctrl + Shift + V'.

Click the 'Alignment' option to access the Alignment drop-down menu.

The Alignment option allows the user to align the positioning of a visual entity or container.

Click the 'Export Image to Clipboard' option to save an image of the current workspace in bitmap format to the operating system clipboard. The bitmap format represents the image as a grid of pixels.

Please Note: For images composed of geometric shapes, bitmap format can be inefficient compared to vector formats, which store coordinates to define lines. If the bitmap images produced for some workspaces in the QSP software are too large, the 'Export Image to Clipboard' option may fail.

Click the 'Export SVG' option from the drop-down menu to export and save the SVG file under its current name. When the 'Save As' pop-up screen appears, choose the relevant folder to save the SVG file. Click the 'Save' button to save the workspace file (.svg file type). Alternatively, modify the File name field before clicking 'Save'.

The SVG format is a text-based format based on Extensible Markup Language (XML) that hierarchically describes images as collections of geometric elements, such as lines and rectangles.

An SVG representation of the workspace produced by the QSP IG software includes all key elements and displays them similarly to their appearance within the software. However, an exact reproduction is not always guaranteed.

Click the 'Unit System' option to open the Unit System modal.

The Unit System modal contains three tabs:

The Base Units modal displays a list of the seven fundamental units integral to the QSP Designer application. To define a different unit of the same dimensionality, click on a base unit option and select the alternative unit displayed in the 'Simulation Base Unit' box.

The Prefixes modal showcases a list of commonly used prefixes that are inherent to the QSP Designer application. These prefixes are fundamental to the application's functionality and are used consistently throughout.

The Derived Units modal displays a list of units that are calculated from combinations of other units, numerical values, and/or prefixes. These derived units are an essential part of the QSP Designer application, providing users with a comprehensive set of measurement options.

Derived units are units that are created by combining other units, numbers, or prefixes. They are used to express quantities in a more convenient or meaningful way. For example, velocity can be expressed as meters per second (m/s), which is a derived unit created by combining the unit of length (meters) with the unit of time (seconds).

The Derived Units modal in QSP Designer provides users with a list of pre-defined derived units that can be used to create custom models and simulations. These derived units can be used to express complex quantities in a more intuitive and user-friendly way.

To access the Image Repository modal, click on the 'Image Repository' option. This will open a centralized location where you can store, organize, and manage your images within the application.

In this modal, you can upload new images, edit existing ones, and use them in your projects. The Image Repository provides a convenient way to manage your visual assets and streamline your workflow.
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The available images are displayed in a list, each accompanied by a preview modal for the selected image. The 'In Use' column indicates whether an image is currently utilized in the model. All images have a displayed name, which can be edited by overwriting the name in the 'Name' box and clicking the 'Apply' button.

Click the 'Search' option to open the Search modal.

Two types of searches can be performed on a loaded QSP workspace:

Click the 'Grids' option to open the Grids modal, which offers a convenient way to browse model entities of a specific type.

The Grids modal is presented as two tabs similar to the palette:

Clicking a tab displays the available models and their associated output properties in a column format, with each row representing a single model or Module entity.

Click the 'Grids (Composite)' option to open the Composite Grids modal, which provides a detailed, read-only grid view of the final workspace. This modal combines all imported workspaces, incorporates substitutions for sub-graphs and weak cloning, and removes all deactivated entities, offering a comprehensive overview of the workspace's final state.

Select the 'Index Order' option to open the Index Order modal.

The order of the indices associated with the selected species can be modified by clicking the relevant option. The primary purpose of the Index Order modal is to enable users to control the unrolled names of indexed quantities used in expressions (e.g., reaction rates), allowing them to choose between formats like 'Species1_up_right' or 'Species1_right_up'. The specified index order influences the arrangement in grids, the property inspector, and the sequence in which variables appear in arrays within the generated ODE scripts.

Click the 'Imported Workspaces' option to open the Imported Workspaces modal.

The Imported Workspaces window comprises two tabs:

The details tab shows textual information about all the workspaces and any issues found with them.

The Graph tab displays a graph showing the relationships between

workspaces.

The Details screen displays a list of all workspaces, including the currently loaded one labeled 'Main. '

'Main' is the workspace that sets properties like the simulation duration for the final model.

The list also provides summary information about the status of the following background checks on imported workspaces:

Below the list of workspaces, the results of three additional overall checks for all workspaces are displayed:

The Graph Screen displays a graph where nodes represent all the workspaces that comprise the final model. Global imports are shown as green edges with dotted lines, while private imports are depicted as solid blue edges with a mid-node labeled with the workspace import node name. Private import cycles are indicated by red edges. A legend is provided to explain the various types of nodes and edges.

Select the 'Workspace Edits' option to reveal the drop-down menu.

The Workspace Edits option allows users to edit the following workspace functions:

Select the 'Configuration' option to open the Configuration modal.

The Engine Version, Default Workspace Extension, and Workspace Save Type can be chosen from the drop-down menus available in this modal.

The Standalone Engine facilitates the execution and generation of solutions for implicit ODE equations within the workspace. By selecting this engine, users can run simulations without needing to connect the QSP Designer software to the Simcyp Simulator, albeit with some limitations. Additionally, it supports the import of virtual populations for simulation purposes.

Choose the 'Standalone' option from the 'Engine Version' drop-down menu to direct the QSP Designer software to run simulations using the Standalone Engine.

In the 'Default Workspace Extension' drop-down menu, select the 'qsp' file extension. This enables advanced mechanistic modeling techniques for predicting clinical outcomes and exploring therapeutic strategies in Certara's Quantitative Systems Pharmacology (QSP) software.

Check the 'Enable Individual Termination Override' box to allow individual termination overrides. This feature lets you customize termination settings for specific cases, providing greater flexibility and control over the termination process.

Check the 'Enable Model Debugging Diagnostics' box to activate the Model Debugger. This feature allows you to run simulations with enhanced inspection and control compared to standard simulations.

Software crashes or unexpected shutdowns can lead to unsaved work being lost. To prevent this, QSP Designer offers users control over the auto-saving of backups, including the option to enable or disable it and set the frequency of backups.

If auto-saving of backups is enabled, the application will save a copy of the current workspace at the specified intervals. Upon shutdown, the backup file for the session will be deleted. However, if the application does not shut down correctly, the backup file will remain on disk and can be loaded in a later session.

The 'Manage Auto-Saved Backups' modal may be accessed via the Auto-Saved Backups item on the File menu that displays all the available backups and allows the user to load any one of them or delete all of them.

The 'Defaults' modal window lets users configure default settings for model parameters and simulation settings, streamlining their workflow.

The Defaults options allow the user to modify the default settings of the QSP Designer entities.