Version 12 Update 1

Downloads:

• Full setup

  MD5-Hash	SHA256-Hash
  6ebe9782e99cd3df086c1bb9892589cd	33f877bc926c5c3fe2634183a51938039b91664a23c545d201b2a6b8f061a531

  

• ospsuite R package

• Gene expression database (human)

  • Additional gene expression databases for human and animal species can be found here.

Portable versions of PK-Sim and MoBi

Portable versions provide an alternative way to use the tools if for some reason the full installation of the OSP software suite is not practical.
No installation is required: just download and extract the zip archives and run PKSim.exe or MoBi.exe from the extracted folder.

• Download PK-Sim 12.1 portable version
• Download MoBi 12.1 portable version

Notes for Portable Versions:

1. Portable versions do not affect the installed OSP Suite and do not interfere with each other.

2. If you only need one tool (e.g. only PK-Sim) - there is no need to download another portable tool(s).

3. PK-Sim and MoBi rely on some common Windows components: .NET Framework and C++ Runtime redistributable.
   In most cases these components are already installed on the target machine. In the very unlikely case that they aren't:

   • If PK-Sim (or MoBi) Portable crashes immediately on startup: The .NET Framework is missing. Download and install it from here.
   • If the program starts and you can create a simulation, but running a simulation crashes: The C++ Runtime is missing. Download and install it from here.

4. If you use the functionality "Send to MoBi" in PK-Sim: you have to enter the location of MoBi.exe (portable) in the program options (same vice versa for MoBi).

5. When you double-click PK-Sim or MoBi project in Windows Explorer - it will always start the installed application (the one installed with the full OSP Suite setup), not one of the portables.

6. If you are using the OSP Qualification Runner (as part of the OSP Qualification Framework) - the path to the portable PK-Sim folder must be passed as an argument, otherwise the installed version will be used.

Release Notes for the Open Systems Pharmacology Software Suite 12 Update 1

New features

MoBi: Trace Source of Parameters and Molecule Initial Values in Simulations

Previously, determining why a parameter (or an initial molecule amount) had a certain value in a simulation could be difficult because definitions might come from several sources (Spatial Structure, Parameter Values, Initial Conditions, Individuals, Expression Profiles, etc.).

With MoBi 12.1, you can now trace the origin of these values in the simulation:

• View the originating module and building block
• Identify the type quickly via an icon in the “Building Block” column
• Distinguish between competing definitions and understand which one was applied

Scope and applicability:

• Available for simulations newly created (or rebuilt) in MoBi 12.1.
  
  Existing simulations from earlier versions must be recreated to expose traceability details.
• Applies to parameters and initial values of molecule amounts.

Benefits:

• Faster troubleshooting of unexpected values
• More transparent scenario refinement
• Reduced risk of misconfiguration when reusing modules

MoBi: Spatial Structure with Individual selection for preview

Adds a way to select a specific individual for preview in the spatial structure view. This feature enables users to visualize individual-specific settings directly within the spatial structure, thereby improving model personalization and analysis.

In this preview mode, individual parameters are shown as read-only within the spatial structure, but the user can quickly navigate to the parameter definition within the individual for editing.

PK-Sim and MoBi: Concurrent Execution of Simulations

Previously, starting a simulation locked the entire user interface until the run completed. This is no longer the case. Now, only simulations that are currently running are locked against modification; all other simulations and project elements remain fully editable.

While one or more simulations are running, you can, for example:

• Start additional simulation runs in parallel
• Create, edit, or view charts
• Create new simulations
• Adjust settings or parameters of simulations that are not currently running

Stopping Simulations

• To stop all currently running simulations at once, click the Stop All Simulations button:

  

• To stop a single simulation, use the context menu of that simulation in the Simulations Explorer:

  

Progress Indicator

When more than one simulation is running, the progress bar displays the number of active simulations:

PK-Sim and MoBi: Batch Edit Mode for Charts

Editing charts with many data points or numerous curves could previously feel slow because every single modification (style change, axis setting, visibility toggle, etc.) triggered an immediate re-render. The new Batch Edit Mode lets you pause automatic chart updates, perform multiple edits, and then apply them all at once—greatly improving responsiveness for large datasets.

Key Capabilities

• Temporarily disables live chart re-drawing while you adjust multiple curves or settings.
• Clear visual indication that the chart is out of date (so you don’t lose track).
• One-click (re)activation applies all accumulated changes in a single re-render.

Typical Workflow

1. Disable auto-update in the Chart Editor.

   

2. Make one or more changes (e.g., add/remove curves, adjust appearance, change axes). After the first modification, the chart is marked as inactive/out-of-date with a hint overlay.

   

3. Re-enable auto-update. All pending modifications are applied at once and the chart refreshes.

   

Exports chart to png

A highly requested feature, this adds the ability to export any chart directly to a PNG file for use in presentations or publications. The implementation supports custom formatting and watermark settings, similar to the "copy to clipboard" function.

MoBi: Create Subfolders possible for modules

Enables users to organize modules by creating subfolders.
This feature is especially useful when working with multiple structural models, helping to keep the workspace tidy and navigable.

MoBi: Save/load neighborhood

Users can now save a neighborhood configuration to a PKML file and load it from PKML. This supports efficient reuse and sharing of neighborhood setups, streamlining workflows for complex modeling scenarios.

PK-Sim and MoBi: Calculation of sensitivity in PI should be interruptable

Sensitivity calculations in parameter identification (PI) can now be interrupted by the user, similar to regular simulation runs. This saves time and resources, allowing users to halt long or unneeded calculations without waiting for them to finish.

OSP Platform qualification library and PBPK Models Library

PBPK Models library extended

New PBPK models added:

• Propofol

Model building process and model quality of every new PBPK model is documented in the corresponding model evaluation report.

New releases of OSP Platform qualification library and PBPK Models Library

As with every new OSP Suite release, ALL platform qualification reports and model evaluation reports have been recreated with the new version of the OSP Suite:

• OSP Qualification Reports library
  • See the Release Notes for a full list of changes.
• OSP-PBPK-Model-Library
  • See the Release Notes for a full list of changes.

New release of the ospsuite R package

• Installation and new features: s. here
• Documentation: s. here

New release of the tlf R package

• Installation and new features: s. here
• Documentation: s. here

Fixed issues and Improvements

PK-Sim

• Hexadecimal value 0x1F is an invalid character
• Population simulations: wrong geoSD calculation
• Parameters under Applications not found when importing from older snapshot

MoBi

• Expression profiles missing in MoBi unless individual is opened in PK-Sim
• Invalid paths in event assignments throws unhandled exception
• Simulation view - show the "Parameters" tab by default instead of "Properties"
• Typing container name not possible after choosing parent path
• Copy path of a parameter/container in the simulation
• Throw a warning message for non-existing neighbourhood
• Export of comparison results fails
• Add protein expression to Parameter Values does not always assign value
• "Negative values allowed" check box behavior
• Error when adding reaction parameter and canceling in PK-Sim module
• Extend PV BB with expression profiles - wrong formula for plasma expression
• Initial conditions BB: Extend from BB and select an Expression Profile
• Rollback crashes in specific scenario
• Load Initial Conditions BB: select exported Expression Profile
• Parameter identification: renaming a parameter makes transfer of results impossible
• Observed data: Multi-select folders and Group by
• Errors in PI sensitivity calculation not obvious to user
• Silent crash when creating a circular reference
• TIME alias reset
• Events BB get no red mark when out of date
• Cannot select relative or absolute in events and spatial structure parameter edit
• Wrong behavior cancelling Dimension Select #3 in Data Importer
• Wrong behavior in observed data importer
• Event assignment paths cannot be resolved
• Can't open existing project, Error: hexadecimal value 0x1F, is an invalid character
• Creating a new physical container does not create MoleculeProperties node
• Undo of clone simulation throws exception
• Closing a simulation takes too long

PK-Sim and MoBi

• Observed data: Multiselect folders and "Group by"
• Opening a new file does not drop imported data in Data importer
• Error when selecting "Link Data To Simulations"
• Add Tag dialog: focus in the text field
• Allow faster cancel from Parameter Identifications
• Error when importing sheet with empty row
• Dimension "Fraction" resets to "Dimensionless"
• loadDataSetsFromExcel throws unclear error for invalid configuration
• Error when loading a file