Downloads:
-
MD5-Hash SHA256-Hash bd54f297956f4a7383121e54018d15fb
890794e061640e63950b5d2a0dc0e8fe27cd2889889d8dbd456991d546f2343c
-
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.).
- 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.
Notes for Portable Versions:
-
Portable versions do not affect the installed OSP Suite and do not interfere with each other.
-
If you only need one tool (e.g. only PK-Sim) - there is no need to download another portable tool(s).
-
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.
-
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).
-
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.
-
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.
- There are 2 types of modules: PK-Sim Modules and Extension Modules.
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:
-
Modify an existing PK-Sim module. This will automatically convert it to an extension module.
-
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 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.
-
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".
-
Optionally select individual and expression profile(s) to include in the exported organ.
-
Create a new "Tumor" extension module with the "Spatial Structure" and "Initial Conditions" building blocks.
-
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.
-
Rename the "Muscle" container to "Tumor". Be sure to check the "Rename Related Entities" checkbox in the next dialog!.
-
Note that after renaming, the neighborhoods have been renamed accordingly.
-
Open the Initial Conditions building block of the Tumor module and click on "Extend".
-
Create a new simulation and select both modules (make sure that the PK-Sim module is on top!).
-
In the next step, optionally select Individual and Expression Profile(s).
-
Tumor drug concentrations, etc. can now be plotted in the simulation.
New "Changes" tab in MoBi simulations shows all values modified in the simulation
[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.
Extension of formula references concepts
More flexible (generic) referencing of quantities (parameters, molecule amounts) with new path keywords.
- Referencing quantities in neighborhoods:
- Referencing quantities in the next/previous lumen segment (in "natural" order: stomach to rectum):
- Referencing the lumen segment from "its" mucosa:
- New keywords for the sum formulas:
-
In parent
(Open-Systems-Pharmacology/MoBi#837) -
In children
(Open-Systems-Pharmacology/MoBi#1374)
-
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
New release of the tlf R package
Fixed issues and Improvements
PK-Sim
- Clone of "Compare Results" Charts
- Expression profile inheritance does not work
- Organ volumes not distributed as per default in a pregnancy population
MoBi
- Clone simulation
- Copy-paste formulas
- Event Assignment - allow entering changed path
- Multiselect context menu for Parameter Identifications
- Exporting PKML of a container exports also the neighborhoods of the container and all sub-containers
- Create Neighborhood without the diagram
- Comparison of passive transports: difference in "Create process rate" flag is not shown
- Create process option when configuring a simulation
- Remove parameter type
Property
- Project-wide chart settings
- Support distinct copy and move operations when dropping nodes
- Check formula assignments in events for circular references
- Copy path of a parameter/container in the simulation
- Do not automatically create the "Volume" parameter for physical containers
PK-Sim and MoBi
- Exporting observed data to Excel/CSV ignores LLOQ
- It is possible to create formulas with the same name as existing
- Crash in cloned Parameter Identification after project save/load
- Data importer: error when "Reload under the same settings"
- Simulations that error while running under sensitivity analysis do not show any error message