Explore the File Menu

The File menu in Certara's QSP Designer includes options for managing workspaces and data efficiently.

The File drop-down menu provides the workspace functions.

The 'New' option from the drop-down menu creates a new workspace. If there are unsaved changes in the current workspace, you will be prompted to save them before proceeding.

Click 'Don't Save' if you don't need to save the current workspace.

Click 'Save' if you need to save the current workspace file before a new workspace is created.

Click the 'Cancel' button to close the pop-up dialog and return to the main QSP screen.

Select the 'Open Workspace' option from the drop-down menu to open an existing, valid workspace file.

An 'Open' pop-up will appear, allowing you to select a workspace file from any folder.

Click 'Open' to load the selected .qsp file, replacing the current workspace.

Click the 'Cancel' button to close the pop-up dialog and return to the main screen.

Click 'Recent Workspaces' from the drop-down menu to access a list of up to 10 previously opened workspaces.

Click 'Auto-Saved Back-ups' from the drop-down menu to open the 'Manage Auto-Saved Backups' window.

The 'Manage Auto-Saved Backups' window displays all available backups.

Users can load any backup by clicking the 'Load' button.

Users can delete all backups by clicking the 'Delete All' button.

Click 'Save Workspace As' from the drop-down menu to save the workspace file with its current name.

A 'Save As' pop-up screen will appear, allowing you to save the workspace file to your desired folder.

Click 'Save' to save the workspace file. Alternatively, modify the File name field first, then click 'Save. '

If you modify an existing user workspace file, a message will appear asking if you want to replace the already saved file.

Click the 'Save Workspace' option from the drop-down menu to save the Workspace file under its current name.

Click 'Outputs' from the drop-down menu to open a menu where you can choose the desired output.

There are four options provided:

Click 'Open QSP Results Database' from the menu to select a folder. QSP Designer will then attempt to merge all .db files from that folder and open the Outputs window, presenting the data as if it came from a single database. For this to succeed, all databases must contain consistent data, such as having the same quantities and distinct individual IDs. If the merge fails, an error message will be displayed.

Note that the merged database object in memory only loads the most space-consuming data (i.e., profiles) as needed. This allows it to handle databases that might be too large to fit into working memory. The functionality for saving the results database from the Outputs window is implemented via .NET code, enabling the writing of simulation results databases. To open it, select the relevant .db file and click 'Open. '

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Click 'Analyse Simulation Results CSV Files' from the menu to open the 'Analyse CSV Files' window.

Click 'Open Merged QSP Results Database' from the menu to open a merged QSP results database file. An 'Open' pop-up screen will appear, allowing you to choose a pre-existing QSP Database folder to store the merged databases.

Click 'Merge CSV Files' from the menu to combine all CSV files in the selected folder into a single file, which can then be saved to a location of your choice. For the merge to succeed, all CSV files must have the same column headers (i.e., the same first row). The merged file will include the column headers once, followed by all rows from the original files. An 'Open' pop-up screen will appear, allowing you to choose a folder to store the merged CSV files.

Clicking 'Import Values From File' allows you to import values for quantities, species, and parameters into a workspace. A dialog will appear, enabling you to select the file from which to import the values.

Once the relevant .csv file is selected, click 'Open,' and the QSP Designer IDE will attempt to read the file. If it fails to do so, an error message will be displayed.

Users are notified if the imported values change the workspace state. Additionally, a notification will indicate if some imported values have no effect on simulations because they are overwritten by assignments.

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Click 'Import Values From File to Category' to import values for quantities, species, and parameters into a designated category. The 'Import Values to Category' window will appear, allowing you to select a category from those available in the workspace. If no categories are available, a notification stating 'No Categories Available' will be displayed.

Click the 'Import' button to open a dialog, then select a CSV file. This import process works similarly to the 'Import Values From File' command but only updates quantities within the selected category. If the file contains values for quantities outside the category or lacks values for all quantities within the category (except those overwritten by assignments), a warning will be displayed.

Select the 'Generate' option from the drop-down menu to open a related menu. This menu allows you to choose the desired script to save and generate.

Click the 'Model Script' option from the drop-down menu to open the 'Generate Script' window, which allows the user to select the relevant script from the 'Scripts' screen.

Selecting the 'Generate R Script' or 'Generate R Plus C Script' option prompts the selection of an output path for saving the generated R ODE script or R Plus C Script. After choosing a destination folder, clicking the 'Generate' button saves the script file (.R file type) in that folder. The workspace is automatically verified, and if successful, either an R script or an R Plus C Script is generated. Upon successful generation, a 'Script generation completed successfully' dialog appears.

Selecting the 'Generate Matlab Script' option prompts the selection of an output path to save the generated Matlab script. After choosing a destination folder, clicking the 'Generate' button saves the Matlab Script workspace file (.m file type) in that folder. The workspace is automatically verified, and if successful, a Matlab Script is generated. Upon successful generation, a 'Script generation completed successfully' dialog appears.

Selecting the 'Generate Lua Script' option prompts the selection of an output path to save the generated Lua ODE script. After choosing a destination folder, clicking the 'Generate' button saves the Lua Script workspace file (.lua file type) in that folder. The workspace is automatically verified, and if successful, a Lua script is generated. Upon successful generation, a 'Script generation completed successfully' dialog appears.

Selecting the 'Generate Julia Script' option prompts the selection of an output path to save the generated Julia script. After choosing a destination folder, clicking the 'Generate' button saves the Julia Script workspace file (.jl file type) in that folder. The workspace is automatically verified, and if successful, a Julia script is generated. Upon successful generation, a 'Script generation completed successfully' dialog appears.

A single global location can be set to output all chosen scripts, organized in appropriate sub-folders. Selecting the 'Use same location' option ensures that all generated scripts are saved in a single, designated folder.

The 'Options' tab provides settings to customize the model output. This includes selecting the Model Input Vector, adding script assignment comments, and enabling the output of reaction rates from the pop-up screen.

This tab provides settings for customizing ODE script generation, including the option to use a model input vector. If this option is not selected, an alternate initialization provider class will be generated instead.

The 'Model Input Vector' option provides an alternative way for users to run simulations with parameter values other than those defined in the QSP workspace.

Selection of the ‘Include Assignment Comments’ option ensures that generated scripts include comments that give the expressions for assignments using the original variable names as defined in the QSP workspace.

The 'Model Input Vector' tab provides settings for customizing the model input vector. This includes selecting which quantities to include from those that are suitable for alternate initialization (i.e., those not updated by repeated assignments), as well as specifying the order in which they should appear.

Errors and success/failure of script generation is shown in the form of messages in the dedicated 'Generation Messages' sub-window.

Script generation errors and success/failure messages are displayed in the dedicated 'Generation Messages' sub-window.

Selecting the 'Entities CSV Export' option enables saving the generated CSV Export. A 'Select Folder' pop-up screen appears, allowing directory selection. Clicking the 'Select Folder' button saves the file and creates a date and time-stamped folder for CSV files, each with a header row. These files are compatible with Excel and QSP for highlighting, copying, and pasting. Upon completion, a 'CSV Export Complete!' dialog appears.

Selecting the 'Entities CSV Export (Composite)' option saves the generated CSV Export (Composite). A 'Select Folder' pop-up screen allows directory selection, creating a date and time-stamped folder to store CSV files. Each grid generates a separate CSV file with a header row, compatible with Excel and QSP for highlighting, copying, and pasting. Upon completion, a 'CSV Export Complete!' dialog appears.

Clicking the 'Import File For Category' option generates an import file for a chosen category and saves it. The 'Generate Import File For Category' window appears, offering options to select from the current workspace or the fully processed composite workspace, choose a category, include units, and include quantities overwritten by assignments. After selecting options, clicking the 'Generate' button prompts a dialog to select a folder for saving the Category CSV file.

The 'VPop From Distributions' option generates a VPop file from the current workspace by selecting quantities. Clicking this option opens the 'Generate VPop From Distributions' window, where available parameters can be selected for inclusion in the VPop file.

For each selected parameter, a uniform distribution must be specified in the 'Selected' pane. This can be either 'Continuous' (by entering 'Min' and 'Max' values) or 'Discrete' (via a comma-separated list of values).

Selection of Distribution Parameters.

Input an RNG seed ('Fixed') or select 'Random' for a system clock-derived seed. Enter the number of individuals to generate, then click 'Generate' to populate the table.
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QSP Designer randomly samples one value from each specified distribution for each individual to be generated. Clicking the 'Write VPop' button prompts a dialog to select a folder for storing the generated VPop CSV file.

The 'Workspace Report' option generates a Pop-Up dialog describing the content of the report.

The 'Main Workspace' tab displays the values for the main workspace without processing, showing the current canvas state without subgraph substitutions.

The 'Fully Processed Model' tab provides values for the fully-processed, composite workspace, combining all imported workspaces and substituting subgraphs. The Workspace Report CSV file can be saved by clicking the 'Export CSV' button.

Upon clicking the 'Workspace Comparison' option, the user is presented with the 'Workspace Comparison' window that allows the selection of two saved QSP workspaces for comparison.

The Print button allows the currently selected graph to be printed using available system printers with standard print options.

Clicking the 'Exit' option exits the QSP application. If unsaved edits exist, a 'Save Changes' dialog appears, allowing the Simcyp Workspace file to be saved to a selected folder.

Save Changes Dialog Options:

Please Note: Selecting 'Save' and then cancelling the 'Save Changes' dialog is the same as choosing 'Cancel' and returning to the application.