#16 Mass balance not conserved in parameter-scan-2d

[Matthias König]

Hi Frank,

somehow the parameter-scan-2D SED-ML specification example does not give the correct results with SED-ML webtools. File attached (I send this yesterday, but opening an issue to track this).

It looks like the mass balance is not conserved during steady state calculation. I added the total MKK (unphosphorylated + the 2 phosphorylation states) as plot2 which should be just a flatline, i.e.
MKK + MKK_P + MKK_PP = const
independent of steady state.

M

[Matthias König]

Tellurium gives just the flatline (with some numerical errors), see figure attached. This worked at some point with the webtools.

[Frank Bergmann]

works locally, maybe we ought to change the omex to make it more apparent where it goes wrong.

[Frank Bergmann]

updated omex file labelling the plot, and adding relevant elements to the report

[Frank Bergmann]

I've deployed a new version that takes care of the regression. Thanks

[Matthias König]

This can be closed.

I included your changes in the L1V3 example and updated the SED-ML web tool
figures in the spec.
Thanks.

On Wed, Oct 4, 2017 at 9:55 AM, Frank Bergmann fbergmann@users.sf.net
wrote:

I've deployed a new version that takes care of the regression. Thanks

• [tickets:#16] https://sourceforge.net/p/libsedml/tickets/16/ Mass
  balance not conserved in parameter-scan-2d*

Status: open
Milestone: 1.0
Created: Fri Sep 29, 2017 07:30 PM UTC by Matthias König
Last Updated: Mon Oct 02, 2017 01:45 PM UTC
Owner: nobody
Attachments:

• L1V3_parameter-scan-2d.omex
  https://sourceforge.net/p/libsedml/tickets/16/attachment/L1V3_parameter-scan-2d.omex
  (88.5 kB; application/octet-stream)

Hi Frank,

somehow the parameter-scan-2D SED-ML specification example does not give
the correct results with SED-ML webtools. File attached (I send this
yesterday, but opening an issue to track this).

It looks like the mass balance is not conserved during steady state
calculation. I added the total MKK (unphosphorylated + the 2
phosphorylation states) as plot2 which should be just a flatline, i.e.
MKK + MKK_P + MKK_PP = const
independent of steady state.

M

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--
Dr. Matthias König
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt-University Berlin, Institute of Biology, Institute for Theoretical
Biology
https://www.livermetabolism.com
konigmatt@googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480