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Getting Started.md

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Best practices - Physioligically-based Quantitative Systems Pharmacology/Toxicology models

The OSP software is best suited for the development of complex systems models based on the PBK framework. With the introduction of the modularization concept in version 12, development of such models is even more efficient, transparent, and sustainable. To get the most out of the new concept, the following best practices should be considered.

  • If possible, each compound should be represented as a separate PK-Sim module.
  • PK-Sim modules should never be modified. Any modification and/or extensions should be implemented as separate modules.
  • An extension module should be defined as generic as possible. I.e., it should be compatible with any PK-Sim module with minimal adjustments, if possible.
  • Avoid duplication of information across modules - only implement the differences to other modules!

Where to get PK-Sim and MoBi version 12

OSMOSES (version 12 of the OSPS) is currently under development and has not entered the beta testing phase yet. However, a curious user can download the portable versions of PK-Sim (https://ci.appveyor.com/project/open-systems-pharmacology-ci/pk-sim/branch/develop/artifacts) and MoBi (https://ci.appveyor.com/project/open-systems-pharmacology-ci/mobi/branch/develop/artifacts) to test the new concept. Any feedback will be greatly appreciated. Contributions to this documentation are equally important as reporting bugs (for MoBi: https://github.com/Open-Systems-Pharmacology/MoBi/issues; for PK-Sim: https://github.com/Open-Systems-Pharmacology/PK-Sim/issues) or creating documentation requests/questions (https://github.com/Open-Systems-Pharmacology/OSMOSES/issues).

How does OSMOSES work?

The concept is described in the article "OSMOSES modularization concept".

Project conversion

To get the full advantage of the new modularization concept with the support of individuals and expression profiles in MoBi, you will require a PBPK model created with PK-Sim V12. For PK-Sim project created with previous version, the project must be re-created from a snapshot. Open your project in PK-Sim V12, export it to snapshot, and then re-load from snapshot (see documentation). After this, all simulations in the project will have the new structure and sending them to MoBi will properly transfer the individuals and expression profiles.

2DO #59

Known issues limitations

  • Having more than one VenousBlood organ in the structure (e.g., when adding an offspring structure with a separate VenousBlood), some administration protocols (intravenous infusion) will be applied to both organs, as the TARGET of the infusion process is set to Plasma and VenousBlood (Open-Systems-Pharmacology/MoBi#1406). As a workaround, both organs should have distinct names (e.g., VenousBlood_offspring), or the tag Organism should be added to the container criteria of the transport process.