Integration step size used in parameter estimation task

[Sebastián]

Hi,

I was wondering how to define the step size used by the integrator in the parameter estimation task. I though it would use the one used by the time course task. I tried this with basiCO:

- Initialize integration options

run_time_course(automatic=False, method="lsoda", max_steps=1000000, stepsize=step_size, use_numbers=False)

- Run parameter estimation

run_parameter_estimation(method='Differential Evolution', update_model=True, create_parametersets=True)

However, I've noticed that when I do:
exp_data_par_est, sim_data_par_est = get_simulation_results()

The sampling time of the sim_data_par_est does not match the step_size I had set, so I guess the options from the run_time_course() are not passed to  run_parameter_estimation().

Just wondering if there is a way to change the step size in the parameter estimation task. I ask this since I want to extract values in sim_data_par_est that exactly match the sampling times in  exp_data_par_est. Also, out of general curiosity.

Thanks!

Sebastian

[Sebastián]

PS. I have found that get_simulation_results(values_only=True) does the trick; yet still wondering about how the step size is determined by the integrator in the parameter estimation task.

[Hoops, Stefan (sh9cq)]

Hello Sebastian,

The step size is only used in COPASI to determine the output time
points. It does not effect the simulation and the internals of the
underlying simulation algorithm. For the parameter estimation task the
time points to be computed are given by the experimental data thus
there is no need to specify those by you.

I hope this helps!
Stefan

On Wed, 2024-12-04 at 16:53 -0800, Sebastián wrote:
> PS. I have found that get_simulation_results(values_only=True) does
> the trick; yet still wondering about how the step size is determined
> by the integrator in the parameter estimation task.
> On Thursday, December 5, 2024 at 11:24:31 AM UTC+11 Sebastián wrote:
> > Hi,

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
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Charlottesville, VA 22911

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