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libRoadRunner: A high-performance SBML simulator
http://libroadrunner.org/
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Let users reset species default values #789

Open luciansmith opened 3 years ago

luciansmith commented 3 years ago

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:

matthiaskoenig commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

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.

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matthiaskoenig commented 3 years ago

@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 commented 3 years ago

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.

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.

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

luciansmith commented 3 years ago

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 commented 3 years ago

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

H

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 https://github.com/sys-bio/roadrunner/issues/789#issuecomment-878666223, 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/