ecoli.processes.tf_binding

Transcription Factor Binding

This process models how transcription factors bind to promoters on the DNA sequence.

class ecoli.processes.tf_binding.TfBinding(parameters=None)

Bases: Step

Transcription Factor Binding Step

defaults: Dict[str, Any]

{   'active_to_bound': {},
    'active_to_inactive_tf': {},
    'bulk_mass_data': array([], shape=(1, 0), dtype=object),
    'bulk_molecule_ids': [],
    'cell_density': 1100.0 [g/L],
    'delta_prob': {'deltaI': [], 'deltaJ': [], 'deltaV': []},
    'emit_unique': False,
    'get_unbound': <function TfBinding.<lambda> at 0x7f7d836ed6c0>,
    'n_avogadro': 6.02214076e+23 [1/mol],
    'p_promoter_bound_tf': <function TfBinding.<lambda> at 0x7f7d836ec720>,
    'rna_ids': [],
    'seed': 0,
    'submass_to_idx': {   'DNA': 8,
                          'mRNA': 2,
                          'metabolite': 6,
                          'miscRNA': 3,
                          'nonspecific_RNA': 4,
                          'protein': 5,
                          'rRNA': 0,
                          'tRNA': 1,
                          'water': 7},
    'tf_ids': [],
    'tf_to_tf_type': {}}

name = 'ecoli-tf-binding'

next_update(timestep, states)

ports_schema()

topology

{   'bulk': ('bulk',),
    'bulk_total': ('bulk',),
    'global_time': ('global_time',),
    'listeners': ('listeners',),
    'next_update_time': ('next_update_time', 'tf_binding'),
    'promoters': ('unique', 'promoter'),
    'timestep': ('timestep',)}

update_condition(timestep, states)

See update_condition().