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)[source]
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 0x7fc271021f80>, 'n_avogadro': 6.02214076e+23 [1/mol], 'p_promoter_bound_tf': <function TfBinding.<lambda> at 0x7fc2711b1e40>, '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'
-
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)[source]
See
update_condition()
.
-
defaults: Dict[str, Any]