2.1.1.1. wc_model_gen.eukaryote package

2.1.1.1.1. Submodules

2.1.1.1.2. wc_model_gen.eukaryote.complexation module

Generator for macromolecular complexation submodel for eukaryotes :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-08-02 :Copyright: 2019, Karr Lab :License: MIT

class wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.SubmodelGenerator

Generator for macromolecular complexation submodel

Options: * amino_acid_id_conversion (dict): a dictionary with amino acid standard ids

as keys and amino acid metabolite ids as values
  • codon_table (dict): a dictionary with protein subunit id as key and
    NCBI identifier for translation table as value, the default is 1 (standard table) for all protein
  • cds (bool): True indicates the sequences of protein subunits are complete CDS,
    the default if True
  • beta (float, optional): ratio of Michaelis-Menten constant
    to substrate concentration (Km/[S]) for use when estimating Km values, the default value is 1
calibrate_submodel()[source]

Calibrate the submodel using data in the KB

clean_and_validate_options()[source]

Apply default options and validate options

gen_rate_laws()[source]

Generate rate laws for the reactions in the submodel

gen_reactions()[source]

Generate reactions associated with submodel

2.1.1.1.3. wc_model_gen.eukaryote.core module

Generator for models based on KBs

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-01-07
Copyright:2019, Karr Lab
License:MIT
class wc_model_gen.eukaryote.core.EukaryoteModelGenerator(knowledge_base, component_generators=None, options=None)[source]

Bases: wc_model_gen.core.ModelGenerator

Generator for submodels based on KBs

Options: * id * name * version * component

  • InitializeModel
  • TranscriptionSubmodelGenerator
DEFAULT_COMPONENT_GENERATORS = (<class 'wc_model_gen.eukaryote.initialize_model.InitializeModel'>, <class 'wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator'>, <class 'wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator'>, <class 'wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator'>)[source]
clean_and_validate_options()[source]

Apply default options and validate options

2.1.1.1.4. wc_model_gen.eukaryote.initialize_model module

Initialize the construction of wc_lang-encoded models from wc_kb-encoded knowledge base.

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-01-09
Copyright:2019, Karr Lab
License:MIT
class wc_model_gen.eukaryote.initialize_model.InitializeModel(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.ModelComponentGenerator

Initialize model from knowledge base

Options:

  • culture_volume (float): volume of cell culture; default is 1.0 liter
  • cell_density(float): cell density; default is 1040 g/liter
  • membrane_density (float): membrane density; default is 1160 g/liter
  • cds (bool): True indicates mRNA sequence is a complete CDS; default is True
  • environment (dict): dictionary with details for generating cell environment in the model
  • ph (float): pH at which species will be protonated and reactions will be balanced; default is 7.4
  • check_reaction (bool): if True, reactions will be checked and corrected for proton and charge balance;
    default is True
  • gen_dna (bool): if True, DNA species types and species will be generated;
    default is True
  • gen_transcripts (bool): if True, transcript species types and species will be generated;
    default is True
  • gen_protein (bool): if True, protein species types and species will be generated;
    default is True
  • gen_metabolites (bool): if True, metabolite species types and species will be generated;
    default is True
  • gen_complexes (bool): if True, macromolecular complex species types and species will be generated;
    default is True
  • gen_distribution_init_concentration (bool): if True, initial concentration of species will be generated;
    default is True
  • gen_observables (bool): if True, observables will be generated; default is True
  • gen_kb_reactions (bool): if True, reactions will be generated; default is True
  • gen_kb_rate_laws (bool): if True, rate laws will be generated; default is True
  • gen_environment (bool): if True, cell environment will be generated; default is True
clean_and_validate_options()[source]

Apply default options and validate options

gen_compartments()[source]

Generate compartments for the model from knowledge base

gen_complexes()[source]

Generate complexes for the model from knowledge base

gen_distribution_init_concentrations()[source]

Generate concentrations for the model from knowledge base

gen_dna()[source]

Generate DNAs for the model from knowledge base

gen_environment()[source]

Generate the environment, i.e. temperature, for the simulated cells

gen_kb_rate_laws()[source]

Generate the rate laws for reactions encoded in the knowledge base

gen_kb_reactions()[source]

Generate reactions encoded within KB

gen_metabolites()[source]

Generate metabolites for the model from knowledge base

gen_observables()[source]

Generate observables for the model from knowledge base

gen_parameters()[source]

Generate parameters for the model from knowledge base

gen_protein()[source]

Generate proteins for the model from knowledge base

gen_species_type(kb_species_type, extra_compartment_ids=None)[source]

Generate a model species type and species

Parameters:
  • kb_species_type (wc_kb.SpeciesType) – knowledge base species type
  • extra_compartment_ids (list of str, optional) – compartment ids of additional species that should be created beyond those represented in the KB
Returns:

model species type

Return type:

  • wc_lang.SpeciesType

gen_taxon()[source]

Generate taxon for the model from knowledge base

gen_transcripts()[source]

Generate transcripts (mature RNAs) for the model from knowledge base

inchi_to_smiles_and_props(inchi, ph)[source]
Convert an InChI string to a SMILES string and calculate properties such
as empirical formula, charge and molecular weight
Parameters:
  • inchi (str) – InChI string
  • ph (float) – pH at which the properties should be determined
Returns:

SMILES string wc_utils.util.chem.core.EmpiricalFormula: empirical formula int: charge float: molecular weight

Return type:

str

run()[source]

Run all the components for initializing model from knowledge base

2.1.1.1.5. wc_model_gen.eukaryote.protein_degradation module

Generator for protein degradation submodel for eukaryotes :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-06-11 :Copyright: 2019, Karr Lab :License: MIT

class wc_model_gen.eukaryote.protein_degradation.ProteinDegradationSubmodelGenerator(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.SubmodelGenerator

Generator for protein degradation submodel

Options: * protein_proteasomes (dict): a dictionary with protein species ID

as the key and a list of the names of proteasome complexes that degrade the protein species as value
  • beta (float, optional): ratio of Michaelis-Menten constant
    to substrate concentration (Km/[S]) for use when estimating Km values, the default value is 1
calibrate_submodel()[source]

Calibrate the submodel using data in the KB

clean_and_validate_options()[source]

Apply default options and validate options

gen_rate_laws()[source]

Generate rate laws for the reactions in the submodel

gen_reactions()[source]

Generate reactions associated with submodel

2.1.1.1.6. wc_model_gen.eukaryote.rna_degradation module

Generator for rna degradation submodel for eukaryotes :Author: Yin Hoon Chew <yinhoon.chew@mssm.edu> :Date: 2019-06-11 :Copyright: 2019, Karr Lab :License: MIT

class wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.SubmodelGenerator

Generator for rna degradation submodel

Options: * rna_exo_pair (dict): a dictionary of RNA id as key and

the name of exosome complex that degrades the RNA as value
  • beta (float, optional): ratio of Michaelis-Menten constant
    to substrate concentration (Km/[S]) for use when estimating Km values, the default value is 1
calibrate_submodel()[source]

Calibrate the submodel using data in the KB

clean_and_validate_options()[source]

Apply default options and validate options

gen_rate_laws()[source]

Generate rate laws for the reactions in the submodel

gen_reactions()[source]

Generate reactions associated with submodel

2.1.1.1.7. wc_model_gen.eukaryote.transcription module

Generator for transcription submodels for eukaryotes

Author:Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:2019-01-07
Copyright:2019, Karr Lab
License:MIT
class wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator(knowledge_base, model, options=None)[source]

Bases: wc_model_gen.core.SubmodelGenerator

Generator for transcription submodel

Options: * rna_pol_pair (dict): a dictionary of RNA id as key and

the name of RNA polymerase complex that transcribes the RNA as value, e.g. rna_pol_pair = {

‘rRNA45S’: ‘DNA-directed RNA Polymerase I complex’, ‘mRNA’: ‘DNA-directed RNA Polymerase II complex’, ‘sRNA’: ‘DNA-directed RNA Polymerase II complex’, ‘tRNA’: ‘DNA-directed RNA Polymerase III complex’, ‘rRNA5S’: ‘DNA-directed RNA Polymerase III complex’ }
  • beta (float, optional): ratio of Michaelis-Menten constant to substrate
    concentration (Km/[S]) for use when estimating Km values, the default value is 1
  • beta_activator (float, optional): ratio of effective equilibrium
    dissociation constant of a transcription factor (activator) to the transcription factor concentration (Ka/[TF]) for use when estimating Ka values, the default value is 1
  • beta_repressor (float, optional): ratio of effective equilibrium
    dissociation constant of a transcription factor (repressor) to the transcription factor concentration (Kr/[TF]) for use when estimating Kr values, the default value is 1
  • activator_effect (float, optional): interaction effect between an activator
    and RNA polymerase, which must take the value of 1 and higher, the default value is 1.2
  • polr_occupancy_width (int, optional): number of base-pairs on the DNA occupied
    by each bound RNA polymerase, , the default value is 80
calibrate_submodel()[source]

Calibrate the submodel using data in the KB

clean_and_validate_options()[source]

Apply default options and validate options

gen_rate_laws()[source]

Generate rate laws for the reactions in the submodel

gen_reactions()[source]

Generate reactions associated with submodel

2.1.1.1.8. wc_model_gen.eukaryote.translation_translocation module

2.1.1.1.9. Module contents