Template for BioMASS model construction (biomass.construction.template)

class biomass.construction.template.ode.DifferentialEquation(perturbation)

diffeq(t, y, *x)

Kinetic equations

biomass.construction.template.ode.initial_values()

Values of the initial condition

biomass.construction.template.ode.param_values()

Parameter values

class biomass.construction.template.observable.Observable

Correlating model simulations and experimental measurements.

obs_names

Names of model observables.

Type:

list of strings

t

Simulation time span.

Type:

range

conditions

Experimental conditions.

Type:

list of strings

simulations

The numpy array to store simulation results.

Type:

numpy.ndarray

normalization

• ‘timepoint’Optional[int]

  The time point at which simulated values are normalized. If None, the maximum value will be used for normalization.

• ‘condition’list of strings

  The experimental conditions to use for normalization. If empty, all conditions defined in sim.conditions will be used.

Type:

nested dict

experiments

Time series data.

Type:

list of dict

error_bars

Error bars to show in figures.

Type:

list of dict

class biomass.construction.template.search_param.SearchParam

Specify model parameters and/or initial values to optimize.

class biomass.construction.template.problem.OptimizationProblem

property bounds

Lower and upper bounds on independent variables.

objective(indiv, *args)

Define an objective function to be minimized.

class biomass.construction.template.viz.Visualization

Plotting parameters for customizing figure properties.

cm

Choosing colormaps for cmap.

Type:

matplotlib.colors.ListedColormap (default: matplotlib.colormaps['tab10'])

single_observable_options

Visualization options for time-course simulation (single-observable).

Type:

list of SingleObservable

multiple_observables_options

Visualization options for time-course simulation (multi-observables).

Type:

MultipleObservables

sensitivity_options

Visualization options for sensitivity analysis results.

Type:

SensitivityOptions

static convert_species_name(name)

figure/sensitivity/initial_condition - Sensitivity for species with nonzero initial conditions.

Return type:

str

static set_sensitivity_rcParams()

figure/sensitivity

Return type:

None

static set_timecourse_rcParams()

figure/simulation

Return type:

None

class biomass.construction.template.reaction_network.ReactionNetwork

Reaction indices grouped according to biological processes. This is used for sensitivity analysis (``target``=’reaction’).

static flux(t, y, x)

Flux vector.