Issue with the unit of a model parameter: SBML import

15 views
Skip to first unread message

Deepa

unread,
Oct 13, 2022, 7:19:57 AM10/13/22
to copasi-u...@googlegroups.com
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)

unread,
Oct 13, 2022, 9:10:39 AM10/13/22
to copasi-u...@googlegroups.com
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

unread,
Oct 13, 2022, 9:31:33 AM10/13/22
to copasi-u...@googlegroups.com
Hello Stefan,

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

Thanks a lot,
Deepa

--
You received this message because you are subscribed to the Google Groups "COPASI User Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to copasi-user-fo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/copasi-user-forum/7108ca24a0103d868907f1c9006033e4f7968ad7.camel%40virginia.edu.

Hoops, Stefan (sh9cq)

unread,
Oct 13, 2022, 5:02:45 PM10/13/22
to copasi-u...@googlegroups.com
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

unread,
Oct 14, 2022, 2:53:38 AM10/14/22
to copasi-u...@googlegroups.com
Hi Stefan,

Thank you so much for the clarification.

Best,
Deepa

Reply all
Reply to author
Forward
0 new messages