A technical framework to assess the confidence of specific intended use of the OSP platform was developed (qualification runner and reporting engine). This framework allows for an automatic (re)-qualification workflow of the OSP suite, comprising the following steps:
PBPK model development and verification with observed data
Qualification plan generation
Qualification report generation
In a first step, the respective qualification scenario is saved in a special qualification repository on GitHub. This qualification scenario repository contains a detailed qualification plan that links and combines respective models and data to address the use case that shall be qualified. Therefore, the qualification plan consists of:
Description of potential cross-dependencies between PK-Sim project files (if adequate) (e.g. it is possible to inherit building blocks or simulation parameters)
Observed data sets (needed for model development and verification)
Qualification scenario description text modules
Detailed report settings to describe the generation of charts and qualification measures.
PK-Sim projects, observed data sets, and qualification scenario text modules can, but not necessarily have to, be saved in their own/different repositories and then conveniently be referenced by the qualification plan.
In the next step, the Qualification Runner (stand-alone tool) processes the qualification plan, i.e. all project parts are exported and prepared for the Reporting Engine. The Reporting Engine provides a validated environment (currently implemented in MATLAB®, a transfer to R is in development) for model execution and generates tables and figures for the final qualification report. This report contains the evaluation of the individual PBPK models with observed data (i.e. standard goodness of fit plots, visual predictive checks) and a comprehensive qualification of the specific use case assessing the predictive performance of the OSP suite by means of a predefined set of qualification measures and charts.
The automated execution of the described workflow can be triggered to assess re-qualification in case new data, changes in model structure or parameterization, or new OSP suite releases arise.
Supersaturation
Supersaturation, i.e. the concentration increase of a solution beyond its saturation, can now be simulated for the formulation type particle dissolution. The parameter can be found in the Advanced Parameters Tab of the Compound Building Block. If activated, the effective compound concentration in the intestinal lumen can exceed the solubility defined in the compound. The default value of this new parameter is false meaning that supersaturation is inactivated.
Observer in PK-Sim
Now it is possible to add custom observers in PK-Sim. Workflow for this:
3. Import observer(s) previously exported as PKML in MoBi
4. Add observers during simulation creation
5. Select observers of interest as outputs
Combination of user defined administrations with advanced protocols
Calculation of the Total fraction metabolized
In the past fraction of metabolized dose could be plotted per compartment only.
Now it is also possible to show the total fraction metabolized (= sum of fraction metabolized over all compartments). It can be found under Organism/Total fraction of dose - <Compound name>
Release Notes for the Open Systems Pharmacology Software Suite 8
Important note – read BEFORE installation
User Template Database migration from 7.3 (and below) to 7.4 and above
New features
(Re-)Qualification framework
A technical framework to assess the confidence of specific intended use of the OSP platform was developed (qualification runner and reporting engine). This framework allows for an automatic (re)-qualification workflow of the OSP suite, comprising the following steps:
In a first step, the respective qualification scenario is saved in a special qualification repository on GitHub. This qualification scenario repository contains a detailed qualification plan that links and combines respective models and data to address the use case that shall be qualified. Therefore, the qualification plan consists of:
PK-Sim projects, observed data sets, and qualification scenario text modules can, but not necessarily have to, be saved in their own/different repositories and then conveniently be referenced by the qualification plan.
In the next step, the Qualification Runner (stand-alone tool) processes the qualification plan, i.e. all project parts are exported and prepared for the Reporting Engine. The Reporting Engine provides a validated environment (currently implemented in MATLAB®, a transfer to R is in development) for model execution and generates tables and figures for the final qualification report. This report contains the evaluation of the individual PBPK models with observed data (i.e. standard goodness of fit plots, visual predictive checks) and a comprehensive qualification of the specific use case assessing the predictive performance of the OSP suite by means of a predefined set of qualification measures and charts.
The automated execution of the described workflow can be triggered to assess re-qualification in case new data, changes in model structure or parameterization, or new OSP suite releases arise.
Supersaturation
Supersaturation, i.e. the concentration increase of a solution beyond its saturation, can now be simulated for the formulation type particle dissolution. The parameter can be found in the Advanced Parameters Tab of the Compound Building Block. If activated, the effective compound concentration in the intestinal lumen can exceed the solubility defined in the compound. The default value of this new parameter is false meaning that supersaturation is inactivated.
Observer in PK-Sim
Now it is possible to add custom observers in PK-Sim. Workflow for this:
3. Import observer(s) previously exported as PKML in MoBi
4. Add observers during simulation creation
5. Select observers of interest as outputsCombination of user defined administrations with advanced protocols
Calculation of the Total fraction metabolized
In the past fraction of metabolized dose could be plotted per compartment only.
Now it is also possible to show the total fraction metabolized (= sum of fraction metabolized over all compartments). It can be found under
Organism/Total fraction of dose - <Compound name>Fixed issues and Improvements
PK-Sim and MoBi
PK-Sim
MoBi
MoBi Toolbox for Matlab
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