Certara's QSP Designer V3 streamlines workflows, improves simulation accuracy, and offers greater flexibility with advanced features and an enhanced user interface. Elevate your research with this groundbreaking release.
QSP Notebook Domain-Specific Language Export
This update introduces a new export feature in QSP Designer, enabling the generation of scripts in the QSP Notebook domain-specific language (DSL).
New Features
Export QSP Notebook DSL Scripts: Added functionality to generate scripts in the QSP Notebook DSL.
Generate QSP Notebook Dosing File: New option to create dosing files tailored to QSP Notebook DSL.
Generate QSP Notebook Conversion File: New option to create conversion files for QSP Notebook DSL.
Improvements
Enhanced Options Tab: Improved settings for exporting QSP Notebook DSL scripts.
Expanded Scripts Tab: New section for managing QSP Notebook DSL scripts.
Fixed Issues
Unit System Differences: Addressed issues related to unit system differences between QSP Designer and QSP Notebook DSL.
Model Parameters and Assignments: Improved handling of model parameters and assignments with '_init' suffixes.
Unsupported Model Features: Processed models to remove unsupported features before exporting.
QSP Platform Enhancements
This update highlights new features and improvements, including unit changes, workspace paths, and verification warnings.
New Features
View Recent Quick Searches: Dropdown of successful quick searches from the current session.
Default Solver Step Sampling Option: Checkbox for "every solver step sampling" in the Sampling Times tab.
Read-Only View for Imported Workspaces: Open a read-only view of an imported workspace via context menus.
Indexed Quantity Finder: Right-click context menu item to find all quantities associated with a given index.
Improvements
Unit Changes on Paste: Detailed warnings for unit changes when copying reaction graphs.
Comparing Old and New Connections: Access detailed differences through the Inspect context menu item.
Enhanced Simulation Base Unit Editing Options: Reset button and scaling factor option for automatic determination.
Enhanced Parameter Selection for Fitting: Use "Control" and "Shift" keys for multiple selections.
Expanded Quick Search Dropdown: Show full names of search results.
Fixed Issues
Verification Warning for Redundant Assignments: Alerts for unnecessary assignments.
Improved Handling of Signed Integers: Accurate reflection of "two’s complement" representation.
Improved Handling of Missing Data Overlay Files: Validation errors displayed without error dialog.
Numerical Sorting in VPop Tables: Values sorted numerically rather than alphabetically.
QSP SimBiology Export Improvements
QSP Designer now supports exporting models with conditional assignments, event nodes, and parameterized or indexed stoichiometry expressions to SimBiology, enhancing translation capabilities.
New Features
Export Conditional Assignments: Added functionality to export models with conditional assignments.
Export Event Nodes: Added functionality to export models with event nodes.
Export Parameterized or Indexed Stoichiometry Expressions: Added functionality to export models with parameterized or indexed stoichiometry expressions.
Reverse Rate Property: Introduced a "Reverse Rate" property for reaction nodes.
Improvements
Enhanced Compartment Determination: Improved automatic determination of reaction compartments for forward and reverse components.
ODE Handling: Enhanced handling of ODEs for amounts rather than concentrations.
Fixed Issues
Verification of Reversible Reactions: Improved verification process for workspaces with reversible reactions.
Error Messages: Resolved issues where exporting models displayed error messages unnecessarily.
QSP Improvements to Model Debugger
The model code debugger in QSP Designer has been enhanced to improve debugging capabilities and ease of use.
New Features
Debugging the Initialization Function:
Users can now debug the initialization function, allowing for thorough examination and troubleshooting.
Breakpoints can be set in the initialization function, but conditions cannot be applied until the model is fully initialized.
Search Functionality:
Users can search through the currently displayed function for strings of interest.
The search field is located at the top-right of the function view, with buttons to navigate between matches.
Matching results are highlighted, and the function view auto-scrolls to the focused match.
Improvements
User Interface Changes:
The initialization function now behaves like other debuggable functions, allowing breakpoints to be set.
The Breakpoint Conditions tab in the Break Manager window does not permit the creation of conditions until the initialization function has fully executed.
QSP Further Improvements to VPop Inference
Enhancements to VPop Inference improve the functionality and flexibility of Virtual Populations (VPops) in QSP Designer.
New Features
Treatment Response Functionality:
Added "Treatment response" mode to simulate/analyze each VPop subject against multiple defined treatments.
Works in both fitting mode (mutating parameters to adhere to observations) and non-fitting mode (filter-only).
Gate Definitions:
Users can now define gates manually or using error margins specified in the data file.
Gates can be defined on a per-treatment basis when combined with treatment response functionality.
New Treatment Response Mode:
New option to define treatments from INIT columns in the VPop Inference import page.
Different data file restrictions when the option is selected.
Gate definition screen now includes a "Treatment" drop-down.
Simulation and analysis take treatments into account.
Inclusion statistics calculation considers treatments.
Improvements
Analysis Stage Enhancements:
Optional analysis stage following fitting-based simulation.
More relaxed filter criteria for mutated parameters.
Threshold for passed gates can be set per DV.
Automatic filtering stage option.
Enhanced plotting options and console area management.
Inclusion Probability Calculation:
Improved calculation of inclusion probabilities.
Generalized multivariate empirical distribution.
Ability to plot univariate distributions and virtual population samples.
Parameter Selection Interface:
Updated interface for selecting individual parameters to fit, mimicking the Parameter Estimation wizard.
New Gate Loading Functionality
The ability to load gates from the loaded data file has been added, enhancing the gate definition process in "New simulation" mode.
New Features
Load From Data File Button:
Added to the gate definitions overview screen.
Clears existing gates and loads gates defined in the data file's ERROR columns.
Gate Inference:
Gates are inferred from the ERROR column values or from ERROR_UPPER and ERROR_LOWER columns.
Example for DV "d":
If ERROR/d is present, gates are loaded with:
min = DV/d - e
max = DV/d + e
If ERROR_LOWER/d and ERROR_UPPER/d are present:
min = ERROR_LOWER/d
max = ERROR_UPPER/d
Treatment Association:
If "Defines treatments from INIT columns" is selected, inferred gates are associated with the matching treatment specified by the ID column.
Manual Gate Definition:
The "new gate definition" popup window allows manual gate definition.
Users can enter Time, Min, and Max values directly.
Observation-Based Gates:
Users can select "From observations" to define gates based on Time and Tolerance, calculated from the data file.
VPop Inference - Enhanced Gate Criteria and Analysis Options
Enhancements to VPop Inference improve gate criteria specification and analysis options in QSP Designer.
New Features
Relaxed Gate Criteria in Fitting Mode:
Users can now analyze with less strict gate criteria after fitting, specifying that only a threshold of gates needs to pass.
Improved Filter Criteria Specification:
Expanded analysis options with a dedicated screen for configuring thresholds.
Users can specify filter criteria for all DVs or chosen DVs, allowing different thresholds for different DVs.
Auto-Run Analysis Stage:
Option to automatically run the Analysis stage following simulation.
Default option is ON, but it resets once the VPop Inference window is closed.
Plotting Improvements:
Enhanced plotting options for both treatments mode and non-treatments mode.
Users can hide/show gates and observations, toggle grid lines, switch scales, edit colors, and export to Plotly HTML.
Graphs can be zoomed, and legends toggled on/off with additional information on hover.
Console Message Options:
Options to copy or clear console messages in the VPop Inference analysis screen.
Frequency Distributions for Inclusion Statistics:
New "Frequency" distribution type can be selected for each variable.
Users can define bins with names, min/max values, and weighted frequencies.
Errors in specification are displayed, preventing calculation of inclusion statistics.
Frequency distributions can be saved/loaded from CSV files.
Enhanced Plotting and Comparison for Inclusion Statistics
Enhancements to the inclusion screen improve plotting and comparison of univariate distributions and virtual population samples using calculated inclusion probabilities.
New Features
Compare Button:
Introduced on the inclusion screen, active once the proportionality constant is fitted.
Opens a window for sampling the population using calculated inclusion probabilities.
Sampling Options:
Users can select distributions or variables defined on the main screen.
Acceptance Sampling and Weighted Sampling options initiate sampling of successful individuals from the VPop Inference analysis stage.
Plotting Normal Distributions:
Plots specified empirical distribution (green line) and sampled individuals binned into intervals (blue bars).
Adjustable bin width for better visualization.
Line of best fit for the estimated distribution of sampled individuals (red curve).
Plotting Frequency Distributions:
Two binning modes: "Distribution bins" and "Fine-grained bins."
Distribution bins mode shows sampled individuals binned into empirically defined bins.
Fine-grained bins mode shows individuals binned into smaller intervals, color-coded to reflect empirical bins.
Plot Configuration:
Plots can be exported to Plotly HTML.
Users can toggle grid lines, switch scales, edit colors, zoom, and toggle legends.
Hovering over parts of the graph provides extra information.
Enhanced Parameter Selection Interface in VPop Inference Wizard
The parameter selection interface in the VPop Inference wizard has been updated to resemble the Parameter Estimation wizard, improving usability and functionality.
New Features
Parameter Selection:
Parameters can be selected from the bottom and added to the list of Selected Parameters using arrows.
Bound Enforcement:
Min/Max checkboxes replaced with "Enforce Lower Bound" and "Enforce Upper Bound."
Minimum and maximum input boxes replaced with "Lower Bound" and "Upper Bound."
Save/Load Functionality:
Selection can be saved or loaded from a CSV file using new Save and Load buttons.
Improvements
Parameter Estimation:
All parameters in the Selected Parameters list are estimated during fitting. The previous option to check/uncheck "Estimate" has been removed.