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

Options:

  • selenoproteome_path (str): path to list of genes that produce selenoproteins

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get list of selenoprotein gene IDs 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

abstract 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

Options:

  • media_path (str): path to media composition

  • rrna_18S_seq_path (str, optional): path to sequence fasta file for representative

    18S rRNA

  • rrna_28S_seq_path (str, optional): path to sequence fasta file for representative

    28S rRNA

  • selenoproteome_path (str): path to list of genes that produce selenoproteins

  • metabolite_structure_path (str): path to metabolite structure

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get media details, sequences of 18S and 28S rRNAs, list of selenoprotein gene IDs and metabolite structre 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, media_path=None, read=False, check_reaction=True, submodel_option_generators=None, submodel_generators=None, test_model=None, test_mode=False)[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

  • media_path (str, optional) – path to media composition

  • 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

  • test_mode (bool, optional) – if True, a dfba objective function will be created at during initialization for test purpose; default is False

3.1.1.3.6. h1_hesc.model_gen.metabolism_option module

Option generator for the H1 metabolism submodel :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2020-02-10 :Copyright: 2019-2020, Karr Lab :License: MIT

class h1_hesc.model_gen.metabolism_option.MetabolismOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 metabolism submodel

Options:

  • recycled_metabolites_path (str): path to consumption of small metabolites

  • media_fluxes_path (str): path to measured fluxes

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.protein_degradation_option module

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

class h1_hesc.model_gen.protein_degradation_option.ProteinDegradationOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 protein degradation submodel

Options:

  • selenoproteome_path (str): path to list of genes that produce selenoproteins

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get list of selenoprotein gene IDs for component options

process_data()[source]

Process data component options

3.1.1.3.8. 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

3.1.1.3.9. 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

3.1.1.3.10. h1_hesc.model_gen.translation_translocation_option module

Option generator for the H1 translation_translocation submodel :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-12-12 :Copyright: 2019, Karr Lab :License: MIT

class h1_hesc.model_gen.translation_translocation_option.TranslationTranslocationOptionGenerator(knowledge_base, component_options, options=None)[source]

Bases: h1_hesc.model_gen.core.SubmodelOptionComponentGenerator

Create options for the H1 translation-translocation submodel

Options: * polysome_profile_path (str): path to polysome profiling data * selenoproteome_path (str): path to list of genes that produce selenoproteins

clean_and_validate_options()[source]

Apply default options and validate options

gen_options()[source]

Construct component options

get_data()[source]

Get polysome profiling data and list of selenoprotein gene IDs for component options

process_data()[source]

Process polysome profile data

The total number of ribosomes that are attached to each translating gene is estimated by multiplying the read (TPM) for each polysome fraction by the number of ribosomes in that fraction, which is taken as 3 for the low polysome fraction (that contains 2-4 ribosomes) and 7 in the high polysome fraction (that contains 5 to 8+ ribosomes)(Floor and Doudna, eLife 2016).

The fraction of ribosomes attached to each translating gene is then estimated by normalizing the above, assuming that 0.8 of intracellular ribosomes (Bionumbers: 102344) are in the polysomes.

Because the data (Blair et al, 2017, doi: 10.1016/j.celrep.2017.10.095) was mapped to a different human reference genome, some gene IDs may not match. For genes in the KB where no match is found, if the total fraction from the matched genes is less than 0.8, the remaining fraction is distributed evenly among the unmatched genes. Otherwise, their fractions are set to zero.

3.1.1.3.11. Module contents

Reconstruction building API

Author

Yin Hoon Chew <yinhoon.chew@mssm.edu>

Date

2019-08-22

Copyright

2019, Karr Lab

License

MIT