2.1. wc_model_gen package

2.1.2. Submodules

2.1.3. wc_model_gen.core module

Base classes for generating wc_lang-formatted models from a knowledge base.

Author:Balazs Szigeti <balazs.szigeti@mssm.edu>
Author:Jonathan Karr <jonrkarr@gmail.com>
Date:2018-01-21
Copyright:2018, Karr Lab
License:MIT
class wc_model_gen.core.ModelComponentGenerator(knowledge_base, model, options=None)[source]

Bases: object

Abstract base class for model component generators

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
model[source]

model

Type:wc_lang.Model
options[source]

options

Type:dict
clean_and_validate_options()[source]

Apply default options and validate options

run()[source]

Generate model components

class wc_model_gen.core.ModelGenerator(knowledge_base, component_generators=None, options=None)[source]

Bases: object

Generator for models (wc_lang.Model)

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
component_generators[source]

model component generators

Type:list
options[source]

dictionary of options whose keys are the names of component generator classes and whose values are dictionaries of options for the component generator classes

Type:dict
DEFAULT_COMPONENT_GENERATORS = ()[source]
static analyze_model(self, results)[source]

Prints the standard analysis of simulation results

clean_and_validate_options()[source]

Apply default options and validate options

static gen_rand_min_model_kb(name=None)[source]

Generates a random min model KB

run()[source]

Generate a wc_lang model from a wc_kb knowledge base

Returns:model
Return type:wc_lang.Model
static run_model(model, results_dir, checkpoint_period=5, end_time=100)[source]

Simulates model

class wc_model_gen.core.SubmodelGenerator(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.ModelComponentGenerator

Base class for submodel generators

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
model[source]

model

Type:wc_lang.Model
submodel[source]

submodel

Type:wc_lang.Submodel
options[source]

options

Type:dict
clean_and_validate_options()[source]

Apply default options and validate options

gen_mechanistic_rate_law_eq(submodel, specie_type_kb, reaction, beta, half_life, cell_cycle_len)[source]
gen_phenom_rate_law_eq(specie_type_kb, reaction, half_life, cell_cycle_len)[source]
gen_rate_laws()[source]

Choose which rate_law to generate

gen_reactions()[source]

Generate reactions associated with submodel

run()[source]

Generate model components

2.1.4. Module contents