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@Yuri05 Yuri05 released this 10 Feb 17:59
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Downloads:

  • Full setup

    MD5-Hash SHA256-Hash
    bd54f297956f4a7383121e54018d15fb 890794e061640e63950b5d2a0dc0e8fe27cd2889889d8dbd456991d546f2343c
  • ospsuite R package

  • Gene expression database (human)

    • Additional gene expression databases for human and animal species can be found here.
      (NOTE: Validation of these databases is ongoing and not fully complete.).
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.

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] (https://go.microsoft.com/fwlink/?LinkID=863265).
    • 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

New features

New modularization concept in MoBi

Building blocks can be grouped into modules, which allows the definition of sub-models and ultimately provides a much more flexible way of modeling. See the documentation for a detailed description of the new concept.

When exporting a simulation from PK-Sim to MoBi, a PK-Sim module is created.
If this exported model should be extended/modified in MoBi, there are 2 options:

  1. Modify an existing PK-Sim module. This will automatically convert it to an extension module.

  2. Much better: Create new extension module(s) and place all extensions/modifications there. This has several advantages:

    • All modifications to the basic PK-Sim model are clearly visible and can be easily documented, etc.
    • All modifications can be applied to other models exported from PK-Sim ▶ no need for duplication, reduced risk of errors

See the documentation for a detailed explanation of how to combine modules into simulations.

  • Create Individuals and Expression Profiles directly in MoBi (or import from PK-Sim)
    • Individuals and expression profiles can be created in MoBi in the same way as in PK-Sim.
      Image

    • Alternatively, Individuals and Expression Profiles can be exported as PKML in PK-Sim and imported in MoBi.

Individuals and Expression Profiles can be combined with modules in simulations and provide even more modeling flexibility.

Example use case: Adding a tumor "organ" in MoBi 12

  • Export a simulation from PK-Sim to MoBi. This will create a PK-Sim module.
    Image

  • Open the spatial structure of the PK-Sim module, select a tissue organ (e.g. muscle) and export it to pkml, e.g. as "Muscle.pkml".
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  • Optionally select individual and expression profile(s) to include in the exported organ.
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  • Create a new "Tumor" extension module with the "Spatial Structure" and "Initial Conditions" building blocks.
    Image Image

  • In the "Tumor" extension module: open the spatial structure and load the top container from the previously saved file Muscle.pkml. Note that the neighborhoods between muscle and arterial/venous blood are also loaded.
    Image Image

  • Rename the "Muscle" container to "Tumor". Be sure to check the "Rename Related Entities" checkbox in the next dialog!.
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  • Note that after renaming, the neighborhoods have been renamed accordingly.
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  • Open the Initial Conditions building block of the Tumor module and click on "Extend".
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  • Select molecules to be incorporated into the tumor.
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  • Create a new simulation and select both modules (make sure that the PK-Sim module is on top!).
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  • In the next step, optionally select Individual and Expression Profile(s).
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  • The "Tumor" organ will now appear in the simulation.
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  • Tumor drug concentrations, etc. can now be plotted in the simulation.
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New "Changes" tab in MoBi simulations shows all values modified in the simulation

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[Experimental!] Creating individuals and populations with HI (Hepatic Impairment)

The HI algorithm is based on the work of Edginton et al. 2008 and Johnson et al. 2010.
This feature has not yet been fully qualified and is therefore marked as experimental in the software.

Image

Extension of formula references concepts

More flexible (generic) referencing of quantities (parameters, molecule amounts) with new path keywords.

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:

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

MoBi

PK-Sim and MoBi