booldog.continuous.ode_factory

Attributes

logger
ode_classes	transform to ODE class translation
transforms	list of accepted ODE transforms

Classes

ODE	Generic ODE class produced by factory.
BooleCubeODE	An ODE class.
SquadODE	An ODE parent class.

Functions

ode_factory(network, transform, **kwargs)

Create a booldog.ode.ODE from Network.

Module Contents

booldog.continuous.ode_factory.logger

booldog.continuous.ode_factory.ode_factory(network, transform, **kwargs)

Create a booldog.ode.ODE from Network.

Parameters:

• network (Network or BooleanNetwork) – Input network.

• transform (str) – One of accepted transforms. See booldog.ode.transforms or Notes for options.

• **kwargs – Additional arguments and keyword arguments passed to specific ODE class.

Returns:

ode – A ODE system

Return type:

booldog.ode.ODE

Notes

For specific transforms, see the relevant class for keyword arguments (**kwargs).

The class per transform is defined in booldog.ode.ode_classes.

If the parameter is an int or float, the value is assigned for all variables. Otherwise the parameter argument should be a dict with keys as node names and values for their initial state. In this case, if the initial state is not defined for all nodes, a default key with the default value should also be present in the dict.

Here follows a summary of the transform-specific keyword arguments

‘squad’

• booldog.ode.SquadODE

• gamma : self-decay

• h : sigmoid gain

‘boolecube’

• booldog.ode.BoolCubeODE

• tau : life-time of species

‘hillcube’

• booldog.ode.BoolCubeODE

• tau : life-time of species

• n : Hill coefficient

• k : Hill dissociation constant

‘normalisedhillcube’

• booldog.ode.BoolCubeODE

• tau : life-time of species

• n : Hill coefficient

• k : Hill dissociation constant

class booldog.continuous.ode_factory.ODE(network, transform)

Generic ODE class produced by factory.

Parent class is a variable, and defined by transform argument.

n

boolean_network

transform

event_function(t, x, event_t, *args)

Event function for events of scipy.integrate.solve_ivp.

Parameters:

• t (float) – Time-point of simulation

• x (narray)

• event_t (float) – Time-point of event

• *args – ignored

terminal

Type:

True

update(off_nodes=None)

Resets dxdt

Shortcut to ODE class’s _get_system method.

Parameters:

off_nodes (list of int, optional) – List of node indices to set derivative to 0, i.e. these nodes will remain constant in simulation.

class booldog.continuous.ode_factory.BooleCubeODE(network, transform, tau=1, n=3, k=0.5, **kwargs)

Bases: ODE

An ODE class.

Use of multivariate polynomial interpolation for the transformation of a

Boolean graph to a system of ODEs.

dxdt

Type:

function

param_tau

life-time of species

Type:

arraylike

param_n

Hill coefficient

Type:

arraylike

param_k

Hill dissociation constant

Type:

arraylike

param_dict

track parameters

Type:

dict

param_n

param_k

param_tau

param_dict

B1

dxdt

hill(x_array)

normalised_hill(x_array)

identity(x_array)

_get_system(off_nodes=None)

homologue_b1()

Create function to calculate the multivariate polynomial interpolation of Boolean functions

Returns:

B1

Return type:

function

write_c_code()

class booldog.continuous.ode_factory.SquadODE(network, transform, gamma=1, h=10, **kwargs)

Bases: ODE

An ODE parent class.

Use of SQUAD for the transformation of a Boolean graph to a system of ODEs.

dxdt

Type:

function

param_gamma

decay rate

Type:

arraylike

param_h

sigmoidal gain

Type:

arraylike

activations

activator matrix

Type:

arraylike

inhibitions

inhibitor matrix

Type:

arraylike

param_gamma

param_h

_A1

_a1

_B1

_b1

dxdt

_omega(x)

Equation (2) of Di Cara et al (2007) http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-462 Based on Andre Blejec R code.

_dxdt_transform(x, w)

Equation (2) of Di Cara et al (2007)

_get_system(off_nodes=[])

booldog.continuous.ode_factory.ode_classes

transform to ODE class translation

Type:

dict

booldog.continuous.ode_factory.transforms

list of accepted ODE transforms

Type:

set