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Parameters defined by ODE: Parameter Values or Initial Conditions #15
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No, I disagree, for a modeller, if a parameter is defined as a state-variable, the "initial value" you then have to specify should also be listed as "initial condition". We might need to aligning the nomenclature "initial value" / "initial condition" |
In this case: if an entry for molecule A in container B is not present in the list, then this molecule has status "not present" in this container. What about the parameter? How does this work together with the idea of only listing parameter whose values are changed? |
Didn't we say we didn't have IC anymore?
I think no one complained about scale factor for Parameter and it's safe to
assume than no one really missed it
…On Tue., Jan. 28, 2020, 5:54 a.m. Pavel Balazki, ***@***.***> wrote:
In this case: if an entry for molecule A in container B is not present in
the list, then this molecule has status "not present" in this container.
What about the parameter? How does this work together with the idea of only
listing parameter whose values are changed?
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Or are we renaming MSV to IC?
On Tue., Jan. 28, 2020, 7:38 a.m. Michael Sevestre, <michael@design2code.ca>
wrote:
… Didn't we say we didn't have IC anymore?
I think no one complained about scale factor for Parameter and it's safe
to assume than no one really missed it
On Tue., Jan. 28, 2020, 5:54 a.m. Pavel Balazki, ***@***.***>
wrote:
> In this case: if an entry for molecule A in container B is not present in
> the list, then this molecule has status "not present" in this container.
> What about the parameter? How does this work together with the idea of only
> listing parameter whose values are changed?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
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I guess this is a technical issue. This simply means the "initial value" is no longer defined at the parameter (NaN, or there simply is no corresponding UI element), but in the "initial conditions" BB. Also, the R-function "setSpeciesInitialValues" would need to handle parameters that are StateVariables. Again, we might need to change Nomenclature to be precise (e.g. call it "setInitialConditions") |
Correct |
I disagree with the technical issue. Having parameter values potentially in
two places is highly confusing don't you think?
…On Tue., Jan. 28, 2020, 7:53 a.m. esqlabs GmbH, ***@***.***> wrote:
Or are we renaming MSV to IC?
Correct
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Depends who you are asking, I guess (modeller vs lay person). |
my vote: Parameter Values. |
I also vote for Parameter Values, especially with Yuris argument. |
Technically, the (non-ODE) Parameter does not appear in the PV BB by default, but only if changed. Also, I don't think users would switch back and forth between "normal" and "ODE"... … okay... if you all vote like this… but are the ICs of these "ODE" parameters handled with "setSpeciesInitialValue" at the moment? |
I am doing it often...
At the moment? You mean, in the "old" r-toolbox? |
Jop |
I know that we discussed it again, but I cannot remember what was the solution:
Do parameters that are defined by an ODE belong to the list of Parameter Values or Initial Conditions?
It is more logical to list them under Parameter Values, as those are, well, parameters. The only problem is the scale factor - in theory it should be possible to change the scale factor for them, too. However, it was not possible until now, so it would be OK to let it out in the new version?
@Yuri05 @msevestre @StephanSchaller
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