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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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Create a new molecule in a module #30

Closed PavelBal closed 1 week ago

PavelBal commented 3 years ago

Creation of a new molecule in a module.

A property "Molecule type" cane be defined (one selection only):

In the IC list, entries of the newly created molecule for all containers in (all) PK-Sim modules and the module where the molecule is defined are created, based on the default values for "isPresent" and "negative values allowed" defined for the containers.

msevestre commented 3 years ago

How do we deal with other types of molecules ? Metabolite, Complex etc..

StephanSchaller commented 3 years ago

How do we deal with other types of molecules ? Metabolite, Complex etc.

Technically, these are just "tags" but not types in a sense how they are structurally handled in the model.

msevestre commented 3 years ago

@StephanSchaller ??

When I have a complex, it is not an enzyme, and not a transporter. I don't want to set it to Floating. So what's the value of the molecule Type? I don't think this description is complete

StephanSchaller commented 3 years ago

On a technical level, we only need to distinguish between floating and stationary, right? everything else is then a "tag" (or sub-category) for either of these types. But I agree, some more description is required, this was only an "initiation".

PavelBal commented 3 years ago

No I realize that this might not be necessary any more, as with the expression redesign we now have proteins always present in all containers. Lets discuss.