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Open-Systems-Pharmacology / OSMOSES

Open-Source MOdeling framework for automated quality control and management of complex life Science systEms modelS (OSMOSES)
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Explain what is meant in paragraph regarding externsion module #31

Closed msevestre closed 1 week ago

msevestre commented 3 years ago

Each module containing molecules automatically contains default IC entries for these molecules in the PK-Sim module(s) or the combination of all PK-Sim modules with the SS BB within the module.

in https://github.com/Open-Systems-Pharmacology/OSMOSES/wiki/WP2:-Modularization-concept#extension-modules

msevestre commented 3 years ago

@PavelBal I don't quite understand anymore what this means

PavelBal commented 3 years ago

IC is an n x m list, with n the number of (floating) molecules and m the number of containers, holding start values of molecules, the corresponding scaling factors, and the "negative values allowed" property. If an entry for molecule a in container b is not in the list, the molecule is "not present" in this container.

When a new molecule is defined in the Module, there are no entries for this molecule in the IC-BB of the PK-Sim modules. Therefore, when creating a simulation, the new molecule would not be present in any container. The module with the new molecule should therefore have the entries for this molecule (like "Extend" in the current MSV-BB).

Maybe this also helps: https://github.com/Open-Systems-Pharmacology/OSMOSES/issues/30 https://github.com/Open-Systems-Pharmacology/OSMOSES/issues/29