celltx package

Subpackages

• celltx.biolayer package
  • Submodules
  • celltx.biolayer.biolayer module
  • Module contents
• celltx.graphlayer package
  • Submodules
  • celltx.graphlayer.graphlayer module
  • Module contents
• celltx.odelayer package
  • Submodules
  • celltx.odelayer.odelayer module
  • Module contents
• celltx.syslayer package
  • Submodules
  • celltx.syslayer.syslayer module
  • Module contents

Submodules

celltx.functions module

class celltx.functions.Constant(name, expr, latex=None, domain=None, **assumptions)

Bases: sympy.core.symbol.Symbol

default_assumptions = {}

name

class celltx.functions.Selector(name, selector_type, selector, latex=None, domain=None, **assumptions)

Bases: sympy.core.symbol.Symbol

default_assumptions = {}

name

class celltx.functions.Symbol(name, latex=None, domain=None, **assumptions)

Bases: sympy.core.symbol.Symbol

default_assumptions = {}

name

celltx.functions.hill(x, kmin, kmax, x50, n)

celltx.functions.ravel_expression(expr)

celltx.model module

Design, construct, and simulate multiscale models of cell therapies.

class celltx.model.Model(name)

Bases: object

Class which holds abstraction layers that allow model definition, ODE system extraction, and simulation.

name

Name of the model

Type

str

bio

BioLayer instance used for high-level model specification

Type

BioLayer

sys

SysLayer instance used for mid-level model specification. Generated by a BioLayer, or manually specified.

Type

SysLayer

graph

GraphLayer instance used for low-level model specification. Generated by a SysLayer, or manually specified.

Type

GraphLayer

ode

ODELayer instance containing a system of differential equations and logic for their modification and evaluation.

Type

ODELayer

compartment_graph()

visualize_compartments()

celltx.modeller module

Elements for generating, configuring, and evaluating celltx models.

class celltx.modeller.Modeller

Bases: object

Class which holds functions for creating a celltx, model, configuring the model, and postprocessing model simulations.

Subclasses of this class must override the following Modeller methods:

• get_model : generate a celltx.model.Model instance based on the options in self.option. Used to populate self.model.

• configure_model : set up self.model with initial parameter and initial condition values.

• get_model_options : return an array of dictionaries specifying names, descriptions, and options for the kwargs of get_model.

model

Singleton instance of a celltx model generated by calling get_model

Type

celltx.model.Model

readout_funcs

List of functions which take as input a model integration run (model.integrate()).

Type

list[func]

model_options

Dict of key-value pairs representing input values for get_model.

Type

dict

configure_model()

Set initial conditions and parameters of self.model.

static get_model(**kwargs)

Generate a celltx.model.Model instance.

get_model_options()

Return a list of dicts, where each dict has the following key/value pairs:

• ‘name’ : name of the argument to be passed to get_model

• ‘description’ : description of what the argument is for

• ‘values’ : list of acceptable values for the argument, with the default value listed first.

set_model_options(options)

Regenerate the model using a new set of options.

setup()

celltx.util module

celltx.util.format_timedelta(diff)

Module contents

Cell Therapy: Cell CAD framework for dynamically constructing and evaluating multiscale models of cell therapies.