Steady state from parameter scan

[Yonatan Negash]

Hi all,

I have been using COPASI and Basico to simulate models across different parameter ranges. The steady states I have obtained from these parameter scans are very close to each other in value but plotting the time course, they seem to follow similar trajectories and dont seem to be unique steady states.

For example: [1.7][1.8][0.9][0.7][0.9][0.7][0.9] :- these are all steady values reported from 7 different parameter changes for a given species

I am using custom python functions to set up a grid space for parameter search and using the basico function run_steadystate to determine steady state values. I have also used runtc and tried adjusting atol and rtol but I get the same results. Is there any change I should make so these values are reported as one steady state.

Thanks for the help! 

Best,

 Yonatan

[Hoops, Stefan (sh9cq)]

Hello Yonathan,

Without looking at your model I cannot say much. The only thing you
have to know is that the steady-state which COPASI finds with the
Newton method is not necessarily reachable by time course from the
given initial conditions. If you want to assure that the steady-state
is reachable you need to rely only on forward integration when
calculating the steady-state.

Thanks,
Stefan

--
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

[Yonatan Negash]

Hi Stefan,

Thank you for your response. I am running the simulation in basico. Is there a way to specify Newton vs forward integration? Or would I change that setting in the GUI? 

I have attached an example model and script below to give a sense for how I am running this

Best,

 Yonatan

[Frank Bergmann]

You could use something like: 

    set_task_settings(T.STEADY_STATE, settings={'method': {'Use Newton': False, 'Use Integration': True}})

before you run the steady state task, to turn off Newton. You can see all parameters to modify using

   get_task_settings(T.STEADY_STATE)

for convenience, the running the steady state also takes a settings dictionary. 

Frank

[Yonatan Negash]

thanks Frank! If I am running multiple steady state tasks should i set it off each time or will once be enough?

Best,

 Yonatan

[Frank Bergmann]

Hello Yonatan, 

you need to set this setting once per model. So it will persist until you load another COPASI / SBML file.

best

Frank