Virtual bioreactor simulation

Function to run virtual bioreactor simulation models based on specified configurations. There are various simulation events available to model different bioreactor operations.

bioreactormodelling.biosim.new_vb_simulation.run_validation_simulation(data: DataFrame, fitted_model: ModelCoefficients, column_map: ColumnMapping, fit_config: FitConfiguration, specific_productivity: float | None, reset_metabolites: bool = False, feed_compositions: list[Feed] | None = None, metabolic_rates: DataFrame | None = None, metabolic_rate_function: Callable[[float, dict[str, float], dict[str, float], dict[str, float]], list[float]] | None = None, titer_function: Callable[[float, dict[str, float], dict[str, float], dict[str, float], list[float]], float] | None = None, user_defined_growth_factor: Callable[[float, dict[str, float], dict[str, float], dict[str, float]], float] | None = None) → DataFrame

Run a validation simulation using the fitted model and the provided data used to get the result from the fit function.

Parameters:

• data (pandas.DataFrame. The experimental data to be used for the simulation)

• fitted_model (ModelCoefficients. The fitted model coefficients)

• column_map (ColumnMapping. The mapping of the columns in the data to the model variables)

• fit_config (FitConfiguration. The configuration for the fitting)

• specific_productivity (float | None. The specific productivity to be used in the simulation)

• reset_metabolites (bool, optional. Whether to reset metabolites at each event, by default False)

• feed_compositions (list[Feed] | None, optional. The feed compositions to be used in the simulation, by default None)

• metabolic_rates (pandas.DataFrame | None, optional. The metabolic rates to be used in the simulation, by default None)

• metabolic_rate_function (MetabolicRateFunction | None, optional. The function to calculate the metabolic rates, by default None)

• titer_function (ProductivityFunction | None, optional. The function to calculate the titer, by default None)

• user_defined_growth_factor (GrowthFactorFunction | None, optional. The user-defined growth factor function, by default None)

Returns:

• pandas.DataFrame

• The simulated data

bioreactormodelling.biosim.new_vb_simulation.run_vb_simulation(fit_config: FitConfiguration, column_map: ColumnMapping, fitted_model: ModelCoefficients, initial_conditions: dict[str, float], events: list[Event], simulation_duration: float, feeds: list[Feed] | None = None, metabolic_rates: DataFrame | None = None, titer_function: Callable[[float, dict[str, float], dict[str, float], dict[str, float], list[float]], float] | None = None, metabolite_function: Callable[[float, dict[str, float], dict[str, float], dict[str, float]], list[float]] | None = None, user_defined_growth_factor: Callable[[float, dict[str, float], dict[str, float], dict[str, float]], float] | None = None) → DataFrame

Run a virtual bioreactor simulation

Parameters:

• fit_config (FitConfiguration. The configuration for the fitting)

• column_map (ColumnMapping. The mapping of the columns in the data to the model variables)

• initial_conditions (dict[str, float]. The initial conditions for the simulation)

• events (list[Event]. The events to be applied during the simulation)

• simulation_duration (float. The duration of the simulation)

• feeds (list[Feed] optional. The feeds to be used in the simulation, by default None)

• metabolic_rates (pandas.DataFrame optional. The metabolic rates to be used in the simulation)

• titer_function (ProductivityFunction optional. The function to calculate the titer, by default None)

• metabolite_function (MetabolicRateFunction optional. The function to calculate the metabolic rates, by default None)

• user_defined_growth_factor (GrowthFactorFunction optional. The user-defined growth factor function, by default None)

Returns:

• pandas.DataFrame

• The simulated data