SBML without observables specified

[sl6zq]

Hi,

I'm trying to use d2d on my SBML model with my own experimental dataset. I loaded the sbml model using arParseSBML then arLoadModel, which created the model's .def file. In my model's .def file, however, I don't have any observables defined. I tried manually adding in the observables that match with the variable for which I have data. However, I get an error that tells me that the variable is already defined in INPUTS. Do you have any recommendation for resolving this issue? Thank you.

[adrianhauber]

HI Sarah,

could you provide the model .def file that lead to this error?

Best, Adrian

[sl6zq]

Hi Adrian,

Thank you for the reply. I've attached the .def file.

Best, Sarah

On Mon, May 2, 2022 at 4:35 AM Adrian Hauber @.***> wrote:

HI Sarah,

could you provide the model .def file that lead to this error?

Best, Adrian

— Reply to this email directly, view it on GitHub https://github.com/Data2Dynamics/d2d/issues/169#issuecomment-1114622541, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOHYXXPAZ2GNJ5HLEESLSP3VH6HWJANCNFSM5UYZ36IQ . You are receiving this because you authored the thread.Message ID: @.***>

[sl6zq]

Hi Adrian,

I was just wondering if you have found any particular issue with the .def file I sent. I've noticed that an example model like ChenMSB2009 also doesn't have observables specified but was still able to match the variables in the model with those in the data. Thank you!

Best, Sarah

On Mon, May 2, 2022 at 9:03 AM Sung Hyun Lee @.***> wrote:

Hi Adrian,

Thank you for the reply. I've attached the .def file.

Best, Sarah

On Mon, May 2, 2022 at 4:35 AM Adrian Hauber @.***> wrote:

HI Sarah,

could you provide the model .def file that lead to this error?

Best, Adrian

— Reply to this email directly, view it on GitHub https://github.com/Data2Dynamics/d2d/issues/169#issuecomment-1114622541, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOHYXXPAZ2GNJ5HLEESLSP3VH6HWJANCNFSM5UYZ36IQ . You are receiving this because you authored the thread.Message ID: @.***>

[chrischdjan]

Hi Sarah,

could you please try again to provide us with your .def file? It's not included in your reply.

If you get an error that says that the variable is already defined in INPUTS, then you might simply rename the input variable (also in the ODEs/Reactions/Equations) or you rename your observable variable (also in your data).

Regarding the ChenMSB2009 example: There are indeed no observables defined in the model.def. Instead they are defined in the individual .def files of the data sets in the /Data folder. This is the recommended way for using multiple data sets.

[sl6zq]

Hi Christian,

I was able to get the code to read my .def file after renaming the observable variable. Thank you!

Sarah

On Wed, May 4, 2022 at 3:27 AM Christian Tönsing @.***> wrote:

Hi Sarah,

could you please try again to provide us with your .def file? It's not included in your reply.

If you get an error that says that the variable is already defined in INPUTS, then you might simply rename the input variable (also in the ODEs/Reactions/Equations) or you rename your observable variable (also in your data).

Regarding the ChenMSB2009 example: There are indeed no observables defined in the model.def. Instead they are defined in the individual .def files of the data sets in the /Data folder. This is the recommended way for using multiple data sets.

— Reply to this email directly, view it on GitHub https://github.com/Data2Dynamics/d2d/issues/169#issuecomment-1117005298, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOHYXXNTBDBM3DYG2XA2EB3VIIRFTANCNFSM5UYZ36IQ . You are receiving this because you authored the thread.Message ID: @.***>