Transition time

13 views
Skip to first unread message

Deepa

unread,
Jun 16, 2022, 10:08:14 AMJun 16
to COPASI User Forum

Dear All,

Could someone please help me with interpreting the transition times
reported in the results of the steady-state analysis?

I get the following values for my model, but not sure how to interpret these values.


Untitled.png


Thanks a lot for your kind attention,
Deepa

Mendes,Pedro

unread,
Jun 16, 2022, 10:52:33 AMJun 16
to copasi-u...@googlegroups.com
Hi Deepa,

the transition times are metrics that reflect how fast each of the
variables is turning over in the steady state.

the definition is that it is the concentration of the species divided by
the flux that crosses it (ie the sum of all positive fluxes, or
alternatively the absolute value of the sum of all negative fluxes).
This has units of time.

large transition times mean that the corresponding species changes
slowly (so it will react slowly to perturbations)

small transition times mean that the corresponding species changes fast
(so it will react quickly to perturbations)

After a perturbation you should expect the species with the smallest
transtion times to be the first approaching a steady state, and the ones
that have the largest to be the last to approach the steady state.

In your results, NAD and d-glucose are the slowest of the species,
while phosphoenol and 1,3-bisphosphoglycerate 2,6-bisphosphate are the
fastest species.

Pedro

On 6/16/22 10:08, Deepa wrote:
>
> Dear All,
>
> Could someone please help me with interpreting the transition times
> reported in the results of the steady-state analysis?
>
> I get the following values for my model, but not sure how to interpret
> these values.
>
>
> Untitled.png
>
>
> Thanks a lot for your kind attention,
> 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
> <mailto:copasi-user-fo...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/copasi-user-forum/2c18445a-c7a9-4d0c-8b7b-49b704217c4bn%40googlegroups.com
> <https://groups.google.com/d/msgid/copasi-user-forum/2c18445a-c7a9-4d0c-8b7b-49b704217c4bn%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
Pedro Mendes, PhD
Professor and Director
Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
group website: http://www.comp-sys-bio.org

Deepa

unread,
Jun 16, 2022, 1:34:13 PMJun 16
to copasi-u...@googlegroups.com
Hi Prof.,

Thank you so much for the explanation.

Would it be wrong to have a transition time in hours ( i.e for NAD  and d-glucose ) in a model?
The component associated with time is the Vmax values (mM/min). Can we associate the
large transition times to the Vmax's?

Also while running the parameter estimation task using steady-state data, the simulation runs for hours.
I'm not sure if the large transition time could be a problem.

Thanks a lot,
Deepa




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/fe8d00ce-be5c-ce4d-b2c2-dd8ab6957fc2%40uchc.edu.
Reply all
Reply to author
Forward
0 new messages