3.1.1.5. h1_hesc.scaled_down_model package

3.1.1.5.1. Submodules

3.1.1.5.2. h1_hesc.scaled_down_model.kb_core module

Generator for a scaled-down knowledge base of H1 hESCs

Author

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

Date

2020-01-06

Copyright

2020, Karr Lab

License

MIT

class h1_hesc.scaled_down_model.kb_core.KbGenerator(component_generators=None, options=None)[source]

Bases: wc_kb_gen.core.KbGenerator

Generator for the knowledge base

Options: * id * name * version * component

  • TaxonGenerator

  • CompartmentsGenerator

  • ChromosomesGenerator

  • GenesTranscriptsExonsProteinsGenerator

  • RegulatoryModulesGenerator

  • MetabolitesGenerator

  • PropertiesGenerator

  • TranscriptsGenerator

  • MetabolicNetworkGenerator

  • ProteinsGenerator

  • ComplexesGenerator

  • MetabolicReactionKineticsGenerator

  • ProteinModificationsGenerator

DEFAULT_COMPONENT_GENERATORS = (<class 'h1_hesc.kb_gen.taxon.TaxonGenerator'>, <class 'h1_hesc.kb_gen.compartments.CompartmentsGenerator'>, <class 'h1_hesc.kb_gen.chromosomes.ChromosomesGenerator'>, <class 'h1_hesc.kb_gen.genes_transcripts_exons_proteins.GenesTranscriptsExonsProteinsGenerator'>, <class 'h1_hesc.kb_gen.regulatory_modules.RegulatoryModulesGenerator'>, <class 'h1_hesc.kb_gen.metabolites.MetabolitesGenerator'>, <class 'h1_hesc.kb_gen.properties.PropertiesGenerator'>, <class 'h1_hesc.kb_gen.transcripts.TranscriptsGenerator'>, <class 'h1_hesc.kb_gen.metabolic_network.MetabolicNetworkGenerator'>, <class 'h1_hesc.kb_gen.proteins.ProteinsGenerator'>, <class 'h1_hesc.kb_gen.complexes.ComplexesGenerator'>, <class 'h1_hesc.kb_gen.metabolic_reaction_kinetics.MetabolicReactionKineticsGenerator'>, <class 'h1_hesc.kb_gen.protein_modifications.ProteinModificationsGenerator'>)[source]
clean_and_validate_options()[source]

Apply default options and validate options

run()[source]

Generate a knowledge base of experimental data for a whole-cell model :returns: knowledge base :rtype: wc_kb.core.KnowledgeBase

h1_hesc.scaled_down_model.kb_core.main()[source]

Generates a scaled-down knowledge base for H1 hESCs

Returns

knowledge base

Return type

wc_kb.Knowledgebase

3.1.1.5.3. h1_hesc.scaled_down_model.model_core module

Generator for a scaled-down model of H1 hESCs

Author

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

Date

2020-01-08

Copyright

2020, Karr Lab

License

MIT

h1_hesc.scaled_down_model.model_core.main()[source]

Generates a scaled-down model of H1 hESCs :returns: model :rtype: wc_lang.Model

3.1.1.5.4. h1_hesc.scaled_down_model.sim_core module

Simulation of the scaled-down model of H1 hESCs

Author

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

Date

2020-01-14

Copyright

2020, Karr Lab

License

MIT

h1_hesc.scaled_down_model.sim_core.main(sim_results_dir=None, sim_time=None, checkpoint_frequency=1, input_model_path=None, add_rxn_path=None, add_rxn=False, scale_time=0, submodels_to_skip=None, profile=False, verbose=False, object_memory_change_interval=0)[source]

Simulate a whole-cell model of H1 hESCs

Parameters

  • sim_results_dir (str, optional) – path to a directory in which results are stored

  • sim_time (float, optional) – the end time of the simulation (sec); if not provided, the cell doubling time will be used

  • checkpoint_frequency (int, optional) – the number of checkpoints during simulation; if not provided, only the final state is checkpointed

  • input_model_path (wc_lang.Model, optional) – path to a model for simulation; if not provided, a model will be read from a default file

  • add_rxn_path (str, optional) – path to a file storing reactions with a fixed rate that will be added before simulation to produce/consume species listed; if not provided, the default path is used

  • add_rxn (bool, optional) – if True, reactions with a fixed rate will be added before simulation to produce/consume species listed in a file; the default is False

  • scale_time (float, optional) – interval between execution of reactions simulated using Deterministic Stochastic Simulation; default of 0 indicates no scaling

  • submodels_to_skip (list, optional) – list of submodel IDs that will be skipped during simulation; the default is an empty list

  • profile (bool, optional) – whether to output a profile of the simulation’s performance created by a Python profiler

  • verbose (bool, optional) – whether to print success output

  • object_memory_change_interval (int, optional) – event interval between memory profiles of the simulation; default of 0 indicates no profile

Returns

simulated model

Return type

wc_lang.Model

3.1.1.5.5. Module contents

Reconstruction building API

Author

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

Date

2019-08-22

Copyright

2019, Karr Lab

License

MIT