Error for the simulation example in the readme

[johannesnicolaus]

The following error was produced when running the example in the readme

RuntimeWarning: invalid value encountered in double_scalars
  + (y[V.Fn] / x[C.KF31]) ** x[C.nF31]

The code:

from biomass import Model, optimize
from biomass.models import Nakakuki_Cell_2010

model = Model(Nakakuki_Cell_2010.__package__).create()
run_simulation(model, viz_type="average", stdev=True)

I think it is caused by an undefined parameter and thus, I propose changing the model used in the exampleto another model that does not require manual input of parameters, or to pre-input the default parameter for the model.

Please let me know if this is a misunderstanding.

[himoto]

Hi @johannesnicolaus,

Did you perform parameter estimation using optimize() function before running run_simulation(model, viz_type="average", stdev=True)?
You need optimized parameter sets to visualize simulation results like this.

You can get them by running:

from biomass import Model, optimize
from biomass.models import Nakakuki_Cell_2010

model = Model(Nakakuki_Cell_2010.__package__).create()

optimize(model, x_id=range(1, 11))  # getting 10 parameter sets

then, visualize results through:

from biomass import run_simulation

run_simulation(model, viz_type="average", stdev=True)

Cheers,

Hiroaki

[johannesnicolaus]

I see, so basically just a misunderstanding. Thanks!

[himoto]

Anytime!