Issue with the unit of a model parameter: SBML import

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Deepa

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Oct 13, 2022, 7:19:57 AM10/13/22
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Hi All,

I've imported an SBML model into Copasi

In the sbml file, the unit of a parameter is per_mM.
<parameter metaid="meta_GAPD_Keq" sboTerm="SBO:0000281" id="GAPD_Keq" name="Keq GAPD" value="0.497383227406177" units="per_mM" constant="true">
In the user interface, I find this expressed as l/kmol (I was expecting l/mmol). Please have a look at the following snapshot.

image.png

Could someone please suggest if the unit has to be re-expressed in the SBML file?
I think per_mM is interpreted as ml/mol, which translates to l/kmol.

Thanks a lot for your kind attention,
Deepa

Hoops, Stefan (sh9cq)

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Oct 13, 2022, 9:10:39 AM10/13/22
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Hello Deepa,

Can you provide the SBML model so that I can check why you are seeing
the warning.

Thanks,
Stefan


On Thu, 2022-10-13 at 16:49 +0530, Deepa wrote:
> Hi All,
>
> I've imported an SBML model into Copasi
>
> In the sbml file, the unit of a parameter is per_mM.
> <parameter metaid="meta_GAPD_Keq" sboTerm="SBO:0000281" id="GAPD_Keq"
> name="Keq GAPD" value="0.497383227406177" units="per_mM"
> constant="true">
> In the user interface, I find this expressed as l/kmol (I was
> expecting l/mmol). Please have a look at the following snapshot.
>
>
>
> Could someone please suggest if the unit has to be re-expressed in
> the SBML file?
> I think per_mM is interpreted as ml/mol, which translates to l/kmol.
>
> Thanks a lot for your kind attention,
> Deepa
>
--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

Deepa

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Oct 13, 2022, 9:31:33 AM10/13/22
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Hello Stefan,

Sure, I will share the model in a private reply.

Thanks a lot,
Deepa

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Hoops, Stefan (sh9cq)

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Oct 13, 2022, 5:02:45 PM10/13/22
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Hello Deepa,

Thank you for the file. This is a problem in the SBML unit import in
the last release. You can manually correct the unit of Keq GADP to
l/mmol as you suggested.

I have created an issue in our tracker:
http://tracker.copasi.org/show_bug.cgi?id=3123

Thanks,
Stefan

Deepa

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Oct 14, 2022, 2:53:38 AM10/14/22
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Hi Stefan,

Thank you so much for the clarification.

Best,
Deepa

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