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In the implementation of noise scaling (#678), we allow the scaling of the noise in the CLE to be modulated independently for all reactions. In this case, each reaction is associated with one noise-scaling parameter. However, there is not good way to pair the information of which noise scaling parameter scales which reaction (so ordering is used). After discussion with @isaacsas it was suggested that something like:
@begin reaction_network
@noise_scaling_parameters a b
k1, 0--> A, [noise=a]
k2, B --> C
k3, A + B --> C, [noise=a]
k4, C --> A + B, [noise=b]
end
would be useful. Here, for 3 of the reactions, we add a noise scaling parameter. We could also move additional information to this field, like instead of using ⇒ to disable massaction, we could make it a field:
@begin reaction_network
@noise_scaling_parameters a b
k1, 0--> A, [noise=a]
k2, B --> C
k3, A + B --> C, [noise=a, massaction=false]
k4, C --> A + B, [noise=b]
end
Expansion of [...] information across bundles reactions would work identically to as rates do.
A similar way would be needed to add this kind of information when Reaction is called to create reactions programmatically (a kwarg?).
The text was updated successfully, but these errors were encountered:
My one concern in thinking more about this becomes how to then control changing the scaling, for example if someone has a reaction arising from an SBML file how can they add a noise scaling to it?
More generally I wonder if we really need a way to associate an id to a reaction/equation, and then we can have mappings from id to properties within systems which can be altered.
In the implementation of noise scaling (#678), we allow the scaling of the noise in the CLE to be modulated independently for all reactions. In this case, each reaction is associated with one noise-scaling parameter. However, there is not good way to pair the information of which noise scaling parameter scales which reaction (so ordering is used). After discussion with @isaacsas it was suggested that something like:
would be useful. Here, for 3 of the reactions, we add a noise scaling parameter. We could also move additional information to this field, like instead of using
⇒
to disable massaction, we could make it a field:Expansion of
[...]
information across bundles reactions would work identically to as rates do.A similar way would be needed to add this kind of information when
Reaction
is called to create reactions programmatically (a kwarg?).The text was updated successfully, but these errors were encountered: