Skip to content

@compartment/@subsystem/similar option for the DSL #1288

@TorkelE

Description

@TorkelE

Potentially (not fully sure, I don't really work much with this kind of models) it might make hierarchical modelling easier if one could define submodels directly in the DSL.

I.e. for a model of a protein which gets created in the nucleus and transported to the cytosol, one could do something like

@reaction_network begin
    @compartment nucleus begin
        (p,d), 0 <--> X
    end
    @compartment cytosol begin
        d, X --> 0
    end
    k, nucleus.X --> cytosol.X
end

(here we use the @compartment option twice, something we currently do not allow for

Another alternative is to allow subsystems to be interpolated directly into a model

rn1 = ...
rn2 = ...
@reaction_network begin
    @subsystems $rn1 rn2
    ...
end

Right now I am not sure if either actually makes any sense, or has any advantage compared to just writing it out in full. But if there is at some point specific compartment support it might at least be worth considering.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions