Let users reset species default values

[luciansmith]

If the value of a species is not set, roadrunner gives it a default value of 0. Other simulators like Copasi give them a default value of 1!

There's no great way to resolve this, since a lot of extant roadrunner/tellurium models and examples rely on our existing default. So probably the best solution is:

• Create a new user setting, and give it the default value of 'no default': make sure that users explicitly set the values for their species.
• Allow users to set the species default value to 0 or 1, to match past-roadrunner or Copasi.

[matthiaskoenig]

These are invalid (underspecified) models if the species are used to calculate any depending math. Not sure it is a good idea to give any value beside NaN in roadrunner, because it hides obvious problems in the model.

[luciansmith]

Yes, that's what I want the new default to be. However, roadrunner has provided defaults for years (as have other simulators) so it will cause problems if we suddenly remove that feature.

[hsauro]

If I don't set a species concentration I assume it is zero. Imagine having a 100 species, you'd have to assign each one to zero. H

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On Mon, Jul 12, 2021 at 4:02 PM Matthias König ***@***.***> wrote: These are invalid (underspecified) models if the species are used to calculate any depending math. Not sure it is a good idea to give any value beside NaN in roadrunner, because it hides obvious problems in the model. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#789 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIBSDWO6YUKF32TGK26ZZ3TXNX2TANCNFSM5AHSV7ZA> .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org ***@***.*** Books: http://books.analogmachine.org/

[matthiaskoenig]

@hsauro
But this is not a problem of roadrunner, but of the tool creating the SBML model (assumingly antimony?).
So the default should be 0 in antimony thereby creating valid models.

[hsauro]

Yes right, default for zero. To respond to Matthias, it would be a real pain to be forced to initialize every species. A GUI can initialize fields automatically but we can't do that.

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On Mon, Jul 12, 2021 at 4:19 PM Lucian Smith ***@***.***> wrote: Yes, that's what I want the new default to be. However, roadrunner has provided defaults for years (as have other simulators) so it will cause problems if we suddenly remove that feature. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#789 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIBSDXSVE4VGTKIOSQ4W4LTXNZ4RANCNFSM5AHSV7ZA> .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org ***@***.*** Books: http://books.analogmachine.org/

[luciansmith]

Providing defaults is something that I've considered adding to antimony in the past, but haven't ever done. Wherever it was added, it wouldn't be too difficult to do.

[hsauro]

Maybe we should add directives to antimony or expand the language in some way? H

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On Mon, Jul 12, 2021 at 4:33 PM Lucian Smith ***@***.***> wrote: Providing defaults is something that I've considered adding to antimony in the past, but haven't ever done. Wherever it was added, it wouldn't be too difficult to do. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#789 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIBSDT2UQBXGK23RA6PGHTTXN3RDANCNFSM5AHSV7ZA> .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org ***@***.*** Books: http://books.analogmachine.org/