3.1.1.3. h1_hesc.model_gen package

3.1.1.3.1. Submodules

3.1.1.3.2. h1_hesc.model_gen.complexation_option module

Option generator for the H1 complexation submodel :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-08-14 :Copyright: 2019, Karr Lab :License: MIT

class h1_hesc.model_gen.complexation_option.ComplexationOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 complexation submodel

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get data for component options

process_data()[source]

Process data component options

3.1.1.3.3. h1_hesc.model_gen.core module

Generator for the model

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-06-06
Copyright:2019, Karr Lab
License:MIT
class h1_hesc.model_gen.core.H1ModelGenerator(knowledge_base, component_generators=None, options=None)[source]

Bases: wc_model_gen.eukaryote.core.EukaryoteModelGenerator

Generator for the H1 model

Options: * id * name * version * component

clean_and_validate_options()[source]

Apply default options and validate options

class h1_hesc.model_gen.core.OptionComponentGenerator(knowledge_base, component_options, options=None)[source]

Bases: object

Base class for option component generators

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
component_options[source]

component options

Type:dict
options[source]

options

Type:dict, optional
run()[source]

Generate option components

class h1_hesc.model_gen.core.OptionGenerator(knowledge_base, option_generators=None, options=None)[source]

Bases: object

Generator for the options for each submodel generator in the H1 whole-cell model

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
option_generators[source]

option component generators

Type:list of OptionComponentGenerator, optional
options[source]

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

Type:dict, optional
DEFAULT_OPTION_GENERATORS = ()[source]
run()[source]

Generate options for each submodel generator :returns: options for each submodel generator :rtype: dict

class h1_hesc.model_gen.core.SubmodelOptionComponentGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.OptionComponentGenerator

Base class for submodel option generators

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
component_options[source]

component options

Type:dict
options[source]

options

Type:dict, optional
clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get data for component options

process_data()[source]

Process data component options

run()[source]

Generate component options

3.1.1.3.4. h1_hesc.model_gen.initialize_model_option module

Option generator for the H1 model initialization

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-08-19
Copyright:2019, Karr Lab
License:MIT
class h1_hesc.model_gen.initialize_model_option.InitializeModelOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 transcription submodel

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get data for component options

process_data()[source]

Process data component options

3.1.1.3.5. h1_hesc.model_gen.main module

Main for the generator for the model

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-06-06
Copyright:2019, Karr Lab
License:MIT
h1_hesc.model_gen.main.main(model_core_path=None, kb_core_path=None, seq_path=None, read=False, check_reaction=True, submodel_option_generators=None, submodel_generators=None, test_model=None)[source]

Generates a whole-cell model for H1 hESCs

Parameters:
  • model_core_path (str, optional) – path to read/write the model
  • kb_core_path (str, optional) – path to the knowledge base
  • seq_path (str, optional) – path to the genome sequence
  • read (bool, optional) – if True, the model will be generated by deserializing a previously created excel spreadsheet given by the model_core_path, else, it will be generated by running the generator and serializing the output; default is False
  • check_reaction (bool, optional) – if True, reaction will be checked and corrected for proton and charge balance during model generation; default is True
  • submodel_option_generators (list of h1_hesc.model_gen.core.OptionGenerator, optional) – list of submodel generators that will be run
  • submodel_generators (list of wc_model_gen.ModelComponentGenerator, optional) – list of submodel generators that will be run
  • test_model (wc_lang.core.Model, optional) – Model object provided for test purpose only

3.1.1.3.6. h1_hesc.model_gen.rna_degradation_option module

Option generator for the H1 rna degradation submodel :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-06-13 :Copyright: 2019, Karr Lab :License: MIT

class h1_hesc.model_gen.rna_degradation_option.RnaDegradationOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 rna degradation submodel

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get data for component options

process_data()[source]

Process data component options

3.1.1.3.7. h1_hesc.model_gen.transcription_option module

Option generator for the H1 transcription submodel

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-06-07
Copyright:2019, Karr Lab
License:MIT
class h1_hesc.model_gen.transcription_option.TranscriptionOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 transcription submodel

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get data for component options

process_data()[source]

Process data component options

3.1.1.3.8. Module contents

Reconstruction building API

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-08-22
Copyright:2019, Karr Lab
License:MIT