E. coli Simulations
[1]:
# Make sure notebook runs out of vivarium-ecoli directory
import sys, os
notebook_path = sys.path[0][:sys.path[0].index('notebooks')]
sys.path.append(notebook_path)
os.chdir(sys.path[-1])
cwd = os.getcwd()
[2]:
import os
from ecoli.experiments.ecoli_master_sim import EcoliSim, CONFIG_DIR_PATH
from vivarium.core.engine import pf
from vivarium.core.composer import Composite
from vivarium.plots.simulation_output import plot_variables
from vivarium.plots.topology import plot_topology
from ecoli.plots.topology import get_ecoli_nonpartition_topology_settings, get_ecoli_partition_topology_settings
E. coli non-partitioned
initialize EcoliSim from file
[3]:
sim_nonpartition = EcoliSim.from_file(CONFIG_DIR_PATH + "no_partition.json")
sim_nonpartition.total_time = 120
sim_nonpartition.divide = False
sim_nonpartition.progress_bar = False
sim_nonpartition.log_updates = False
sim_nonpartition.raw_output = False
sim_nonpartition.build_ecoli()
print the processes
[4]:
print(pf(sim_nonpartition.ecoli.processes))
{ 'ecoli-chromosome-structure': <ecoli.processes.chromosome_structure.ChromosomeStructure object at 0x10323c730>,
'ecoli-metabolism': <ecoli.processes.metabolism.Metabolism object at 0x1246771c0>,
'ecoli-tf-binding': <ecoli.processes.tf_binding.TfBinding object at 0x12c310d90>,
'ecoli-transcript-initiation': <ecoli.processes.transcript_initiation.TranscriptInitiation object at 0x124677220>,
'ecoli-transcript-elongation': <ecoli.processes.transcript_elongation.TranscriptElongation object at 0x124677190>,
'ecoli-rna-degradation': <ecoli.processes.rna_degradation.RnaDegradation object at 0x12b505070>,
'ecoli-polypeptide-initiation': <ecoli.processes.polypeptide_initiation.PolypeptideInitiation object at 0x12b505190>,
'ecoli-polypeptide-elongation': <ecoli.processes.polypeptide_elongation.PolypeptideElongation object at 0x12dfa35b0>,
'ecoli-complexation': <ecoli.processes.complexation.Complexation object at 0x12b5051c0>,
'ecoli-two-component-system': <ecoli.processes.two_component_system.TwoComponentSystem object at 0x12dfa36d0>,
'ecoli-equilibrium': <ecoli.processes.equilibrium.Equilibrium object at 0x12dfa3820>,
'ecoli-protein-degradation': <ecoli.processes.protein_degradation.ProteinDegradation object at 0x12dfa38b0>,
'ecoli-chromosome-replication': <ecoli.processes.chromosome_replication.ChromosomeReplication object at 0x12dfa3940>,
'ecoli-mass-listener': <ecoli.processes.listeners.mass_listener.MassListener object at 0x12b505130>,
'mRNA_counts_listener': <ecoli.processes.listeners.mRNA_counts.mRNACounts object at 0x12dfa39d0>}
print the topology
[5]:
print(pf(sim_nonpartition.ecoli.topology))
{ 'ecoli-chromosome-structure': { 'listeners': ('listeners',),
'fragmentBases': ('bulk',),
'molecules': ('bulk',),
'active_tfs': ('bulk',),
'subunits': ('bulk',),
'amino_acids': ('bulk',),
'active_replisomes': ( 'unique',
'active_replisome'),
'oriCs': ('unique', 'oriC'),
'chromosome_domains': ( 'unique',
'chromosome_domain'),
'active_RNAPs': ('unique', 'active_RNAP'),
'RNAs': ('unique', 'RNA'),
'active_ribosome': ( 'unique',
'active_ribosome'),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'promoters': ('unique', 'promoter'),
'DnaA_boxes': ('unique', 'DnaA_box')},
'ecoli-metabolism': { 'metabolites': ('bulk',),
'catalysts': ('bulk',),
'kinetics_enzymes': ('bulk',),
'kinetics_substrates': ('bulk',),
'amino_acids': ('bulk',),
'listeners': ('listeners',),
'environment': ('environment',),
'polypeptide_elongation': ( 'process_state',
'polypeptide_elongation'),
'amino_acids_total': ('bulk',)},
'ecoli-tf-binding': { 'promoters': ('unique', 'promoter'),
'active_tfs': ('bulk',),
'active_tfs_total': ('bulk',),
'inactive_tfs_total': ('bulk',),
'listeners': ('listeners',)},
'ecoli-transcript-initiation': { 'environment': ('environment',),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ('unique', 'active_RNAP'),
'promoters': ('unique', 'promoter'),
'molecules': ('bulk',),
'listeners': ('listeners',)},
'ecoli-transcript-elongation': { 'environment': ('environment',),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ('unique', 'active_RNAP'),
'molecules': ('bulk',),
'bulk_RNAs': ('bulk',),
'ntps': ('bulk',),
'listeners': ('listeners',)},
'ecoli-rna-degradation': { 'charged_trna': ('bulk',),
'bulk_RNAs': ('bulk',),
'nmps': ('bulk',),
'fragmentMetabolites': ('bulk',),
'fragmentBases': ('bulk',),
'endoRnases': ('bulk',),
'exoRnases': ('bulk',),
'subunits': ('bulk',),
'molecules': ('bulk',),
'RNAs': ('unique', 'RNA'),
'active_ribosome': ('unique', 'active_ribosome'),
'listeners': ('listeners',)},
'ecoli-polypeptide-initiation': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'RNA': ('unique', 'RNA'),
'subunits': ('bulk',)},
'ecoli-polypeptide-elongation': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'molecules': ('bulk',),
'monomers': ('bulk',),
'amino_acids': ('bulk',),
'ppgpp_reaction_metabolites': ('bulk',),
'uncharged_trna': ('bulk',),
'charged_trna': ('bulk',),
'charging_molecules': ('bulk',),
'synthetases': ('bulk',),
'subunits': ('bulk',),
'polypeptide_elongation': ( 'process_state',
'polypeptide_elongation'),
'molecules_total': ('bulk',),
'amino_acids_total': ('bulk',),
'charged_trna_total': ('bulk',),
'uncharged_trna_total': ('bulk',)},
'ecoli-complexation': {'molecules': ('bulk',), 'listeners': ('listeners',)},
'ecoli-two-component-system': { 'listeners': ('listeners',),
'molecules': ('bulk',)},
'ecoli-equilibrium': {'listeners': ('listeners',), 'molecules': ('bulk',)},
'ecoli-protein-degradation': { 'metabolites': ('bulk',),
'proteins': ('bulk',)},
'ecoli-chromosome-replication': { 'replisome_trimers': ('bulk',),
'replisome_monomers': ('bulk',),
'dntps': ('bulk',),
'ppi': ('bulk',),
'active_replisomes': ( 'unique',
'active_replisome'),
'oriCs': ('unique', 'oriC'),
'chromosome_domains': ( 'unique',
'chromosome_domain'),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'listeners': ('listeners',),
'environment': ('environment',)},
'ecoli-mass-listener': { 'bulk': ('bulk',),
'unique': ('unique',),
'listeners': ('listeners',)},
'mRNA_counts_listener': { 'listeners': ('listeners',),
'RNAs': ('unique', 'RNA')}}
plot the topology
[6]:
ecoli_composite = Composite({
'processes': sim_nonpartition.ecoli.processes,
'topology': sim_nonpartition.ecoli.topology,
})
topology_settings = get_ecoli_nonpartition_topology_settings()
topology_settings['font_size'] = 16
fig = plot_topology(ecoli_composite, topology_settings)
run simulation
[7]:
sim_nonpartition.run()
nonpartition_output = sim_nonpartition.query()
Simulation ID: 199f0850-2d74-11ec-947e-acde48001122
Created: 10/14/2021 at 21:55:22
Completed in 90.93 seconds
[8]:
print(nonpartition_output['listeners']['mass'].keys())
dict_keys(['cell_mass', 'dry_mass', 'water_mass', 'rnaMass', 'rRnaMass', 'tRnaMass', 'mRnaMass', 'dnaMass', 'proteinMass', 'smallMoleculeMass', 'volume', 'proteinMassFraction', 'rnaMassFraction', 'growth', 'instantaniousGrowthRate', 'dryMassFoldChange', 'proteinMassFoldChange', 'rnaMassFoldChange', 'smallMoleculeFoldChange'])
[9]:
# plot
fig = plot_variables(
nonpartition_output,
variables=[
('listeners', 'mass', 'cell_mass'),
('listeners', 'mass', 'dry_mass'),
('listeners', 'mass', 'dnaMass'),
('listeners', 'mass', 'mRnaMass'),
('listeners', 'mass', 'rRnaMass'),
('listeners', 'mass', 'tRnaMass'),
('listeners', 'mass', 'rnaMass'),
('listeners', 'mass', 'proteinMass'),
('listeners', 'mass', 'smallMoleculeMass'),
],
column_width=10, row_height=3, row_padding=0.5)
E. coli master
This model uses partitioning.
initialize EcoliSim from file
[10]:
sim_master = EcoliSim.from_file()
sim_master.total_time = 120
sim_master.divide = False
sim_master.progress_bar = False
sim_master.log_updates = False
sim_master.raw_output = False
sim_master.build_ecoli()
print the processes
[11]:
print(pf(sim_master.ecoli.processes))
{ 'ecoli-chromosome-structure': <ecoli.processes.chromosome_structure.ChromosomeStructure object at 0x124670850>,
'ecoli-metabolism': <ecoli.processes.metabolism.Metabolism object at 0x124670760>,
'ecoli-tf-binding_requester': <ecoli.processes.partition.Requester object at 0x1ad589a60>,
'ecoli-transcript-initiation_requester': <ecoli.processes.partition.Requester object at 0x1ad589a30>,
'ecoli-transcript-elongation_requester': <ecoli.processes.partition.Requester object at 0x1ad589ac0>,
'ecoli-rna-degradation_requester': <ecoli.processes.partition.Requester object at 0x1ad589a90>,
'ecoli-polypeptide-initiation_requester': <ecoli.processes.partition.Requester object at 0x1ad589af0>,
'ecoli-polypeptide-elongation_requester': <ecoli.processes.partition.Requester object at 0x1ad589b20>,
'ecoli-complexation_requester': <ecoli.processes.partition.Requester object at 0x1ad589b50>,
'ecoli-two-component-system_requester': <ecoli.processes.partition.Requester object at 0x1ad589b80>,
'ecoli-equilibrium_requester': <ecoli.processes.partition.Requester object at 0x1ad589bb0>,
'ecoli-protein-degradation_requester': <ecoli.processes.partition.Requester object at 0x1ad589be0>,
'ecoli-chromosome-replication_requester': <ecoli.processes.partition.Requester object at 0x1ad589c10>,
'allocator': <ecoli.processes.allocator.Allocator object at 0x1b8dec6a0>,
'ecoli-tf-binding_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589c40>,
'ecoli-transcript-initiation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589c70>,
'ecoli-transcript-elongation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589ca0>,
'ecoli-rna-degradation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589cd0>,
'ecoli-polypeptide-initiation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589d00>,
'ecoli-polypeptide-elongation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589d30>,
'ecoli-complexation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589d60>,
'ecoli-two-component-system_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589d90>,
'ecoli-equilibrium_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589dc0>,
'ecoli-protein-degradation_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589df0>,
'ecoli-chromosome-replication_evolver': <ecoli.processes.partition.Evolver object at 0x1ad589e20>,
'ecoli-mass-listener': <ecoli.processes.listeners.mass_listener.MassListener object at 0x1dcfd4730>,
'mRNA_counts_listener': <ecoli.processes.listeners.mRNA_counts.mRNACounts object at 0x1b8dec790>}
print the topology
[12]:
print(pf(sim_master.ecoli.topology))
{ 'ecoli-chromosome-structure': { 'listeners': ('listeners',),
'fragmentBases': ('bulk',),
'molecules': ('bulk',),
'active_tfs': ('bulk',),
'subunits': ('bulk',),
'amino_acids': ('bulk',),
'active_replisomes': ( 'unique',
'active_replisome'),
'oriCs': ('unique', 'oriC'),
'chromosome_domains': ( 'unique',
'chromosome_domain'),
'active_RNAPs': ('unique', 'active_RNAP'),
'RNAs': ('unique', 'RNA'),
'active_ribosome': ( 'unique',
'active_ribosome'),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'promoters': ('unique', 'promoter'),
'DnaA_boxes': ('unique', 'DnaA_box')},
'ecoli-metabolism': { 'metabolites': ('bulk',),
'catalysts': ('bulk',),
'kinetics_enzymes': ('bulk',),
'kinetics_substrates': ('bulk',),
'amino_acids': ('bulk',),
'listeners': ('listeners',),
'environment': ('environment',),
'polypeptide_elongation': ( 'process_state',
'polypeptide_elongation'),
'amino_acids_total': ('bulk',)},
'ecoli-tf-binding_requester': { 'promoters': ('unique', 'promoter'),
'active_tfs': ('bulk',),
'active_tfs_total': ('bulk',),
'inactive_tfs_total': ('bulk',),
'listeners': ('listeners',),
'request': { '_path': ( 'request',
'ecoli-tf-binding'),
'active_tfs': ('bulk',)}},
'ecoli-tf-binding_evolver': { 'promoters': ('unique', 'promoter'),
'active_tfs': ('bulk',),
'active_tfs_total': ('bulk',),
'inactive_tfs_total': ('bulk',),
'listeners': ('listeners',),
'allocate': { '_path': ( 'allocate',
'ecoli-tf-binding'),
'active_tfs': ('bulk',)}},
'ecoli-transcript-initiation_requester': { 'environment': ('environment',),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ( 'unique',
'active_RNAP'),
'promoters': ( 'unique',
'promoter'),
'molecules': ('bulk',),
'listeners': ('listeners',),
'request': { '_path': ( 'request',
'ecoli-transcript-initiation'),
'molecules': ( 'bulk',)}},
'ecoli-transcript-initiation_evolver': { 'environment': ('environment',),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ( 'unique',
'active_RNAP'),
'promoters': ('unique', 'promoter'),
'molecules': ('bulk',),
'listeners': ('listeners',),
'allocate': { '_path': ( 'allocate',
'ecoli-transcript-initiation'),
'molecules': ( 'bulk',)}},
'ecoli-transcript-elongation_requester': { 'environment': ('environment',),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ( 'unique',
'active_RNAP'),
'molecules': ('bulk',),
'bulk_RNAs': ('bulk',),
'ntps': ('bulk',),
'listeners': ('listeners',),
'request': { '_path': ( 'request',
'ecoli-transcript-elongation'),
'molecules': ( 'bulk',),
'bulk_RNAs': ( 'bulk',),
'ntps': ('bulk',)}},
'ecoli-transcript-elongation_evolver': { 'environment': ('environment',),
'RNAs': ('unique', 'RNA'),
'active_RNAPs': ( 'unique',
'active_RNAP'),
'molecules': ('bulk',),
'bulk_RNAs': ('bulk',),
'ntps': ('bulk',),
'listeners': ('listeners',),
'allocate': { '_path': ( 'allocate',
'ecoli-transcript-elongation'),
'molecules': ('bulk',),
'bulk_RNAs': ('bulk',),
'ntps': ('bulk',)}},
'ecoli-rna-degradation_requester': { 'charged_trna': ('bulk',),
'bulk_RNAs': ('bulk',),
'nmps': ('bulk',),
'fragmentMetabolites': ('bulk',),
'fragmentBases': ('bulk',),
'endoRnases': ('bulk',),
'exoRnases': ('bulk',),
'subunits': ('bulk',),
'molecules': ('bulk',),
'RNAs': ('unique', 'RNA'),
'active_ribosome': ( 'unique',
'active_ribosome'),
'listeners': ('listeners',),
'request': { '_path': ( 'request',
'ecoli-rna-degradation'),
'charged_trna': ('bulk',),
'bulk_RNAs': ('bulk',),
'nmps': ('bulk',),
'fragmentMetabolites': ( 'bulk',),
'fragmentBases': ('bulk',),
'endoRnases': ('bulk',),
'exoRnases': ('bulk',),
'subunits': ('bulk',),
'molecules': ('bulk',)}},
'ecoli-rna-degradation_evolver': { 'charged_trna': ('bulk',),
'bulk_RNAs': ('bulk',),
'nmps': ('bulk',),
'fragmentMetabolites': ('bulk',),
'fragmentBases': ('bulk',),
'endoRnases': ('bulk',),
'exoRnases': ('bulk',),
'subunits': ('bulk',),
'molecules': ('bulk',),
'RNAs': ('unique', 'RNA'),
'active_ribosome': ( 'unique',
'active_ribosome'),
'listeners': ('listeners',),
'allocate': { '_path': ( 'allocate',
'ecoli-rna-degradation'),
'charged_trna': ('bulk',),
'bulk_RNAs': ('bulk',),
'nmps': ('bulk',),
'fragmentMetabolites': ( 'bulk',),
'fragmentBases': ('bulk',),
'endoRnases': ('bulk',),
'exoRnases': ('bulk',),
'subunits': ('bulk',),
'molecules': ('bulk',)}},
'ecoli-polypeptide-initiation_requester': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'RNA': ('unique', 'RNA'),
'subunits': ('bulk',),
'request': { '_path': ( 'request',
'ecoli-polypeptide-initiation'),
'subunits': ( 'bulk',)}},
'ecoli-polypeptide-initiation_evolver': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'RNA': ('unique', 'RNA'),
'subunits': ('bulk',),
'allocate': { '_path': ( 'allocate',
'ecoli-polypeptide-initiation'),
'subunits': ( 'bulk',)}},
'ecoli-polypeptide-elongation_requester': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'molecules': ('bulk',),
'monomers': ('bulk',),
'amino_acids': ('bulk',),
'ppgpp_reaction_metabolites': ( 'bulk',),
'uncharged_trna': ('bulk',),
'charged_trna': ('bulk',),
'charging_molecules': ('bulk',),
'synthetases': ('bulk',),
'subunits': ('bulk',),
'polypeptide_elongation': ( 'process_state',
'polypeptide_elongation'),
'molecules_total': ('bulk',),
'amino_acids_total': ('bulk',),
'charged_trna_total': ('bulk',),
'uncharged_trna_total': ('bulk',),
'request': { '_path': ( 'request',
'ecoli-polypeptide-elongation'),
'molecules': ( 'bulk',),
'monomers': ( 'bulk',),
'amino_acids': ( 'bulk',),
'ppgpp_reaction_metabolites': ( 'bulk',),
'uncharged_trna': ( 'bulk',),
'charged_trna': ( 'bulk',),
'charging_molecules': ( 'bulk',),
'synthetases': ( 'bulk',),
'subunits': ( 'bulk',)}},
'ecoli-polypeptide-elongation_evolver': { 'environment': ('environment',),
'listeners': ('listeners',),
'active_ribosome': ( 'unique',
'active_ribosome'),
'molecules': ('bulk',),
'monomers': ('bulk',),
'amino_acids': ('bulk',),
'ppgpp_reaction_metabolites': ( 'bulk',),
'uncharged_trna': ('bulk',),
'charged_trna': ('bulk',),
'charging_molecules': ('bulk',),
'synthetases': ('bulk',),
'subunits': ('bulk',),
'polypeptide_elongation': ( 'process_state',
'polypeptide_elongation'),
'molecules_total': ('bulk',),
'amino_acids_total': ('bulk',),
'charged_trna_total': ('bulk',),
'uncharged_trna_total': ('bulk',),
'allocate': { '_path': ( 'allocate',
'ecoli-polypeptide-elongation'),
'molecules': ( 'bulk',),
'monomers': ('bulk',),
'amino_acids': ( 'bulk',),
'ppgpp_reaction_metabolites': ( 'bulk',),
'uncharged_trna': ( 'bulk',),
'charged_trna': ( 'bulk',),
'charging_molecules': ( 'bulk',),
'synthetases': ( 'bulk',),
'subunits': ( 'bulk',)}},
'ecoli-complexation_requester': { 'molecules': ('bulk',),
'listeners': ('listeners',),
'request': { '_path': ( 'request',
'ecoli-complexation'),
'molecules': ('bulk',)}},
'ecoli-complexation_evolver': { 'molecules': ('bulk',),
'listeners': ('listeners',),
'allocate': { '_path': ( 'allocate',
'ecoli-complexation'),
'molecules': ('bulk',)}},
'ecoli-two-component-system_requester': { 'listeners': ('listeners',),
'molecules': ('bulk',),
'request': { '_path': ( 'request',
'ecoli-two-component-system'),
'molecules': ( 'bulk',)}},
'ecoli-two-component-system_evolver': { 'listeners': ('listeners',),
'molecules': ('bulk',),
'allocate': { '_path': ( 'allocate',
'ecoli-two-component-system'),
'molecules': ( 'bulk',)}},
'ecoli-equilibrium_requester': { 'listeners': ('listeners',),
'molecules': ('bulk',),
'request': { '_path': ( 'request',
'ecoli-equilibrium'),
'molecules': ('bulk',)}},
'ecoli-equilibrium_evolver': { 'listeners': ('listeners',),
'molecules': ('bulk',),
'allocate': { '_path': ( 'allocate',
'ecoli-equilibrium'),
'molecules': ('bulk',)}},
'ecoli-protein-degradation_requester': { 'metabolites': ('bulk',),
'proteins': ('bulk',),
'request': { '_path': ( 'request',
'ecoli-protein-degradation'),
'metabolites': ( 'bulk',),
'proteins': ('bulk',)}},
'ecoli-protein-degradation_evolver': { 'metabolites': ('bulk',),
'proteins': ('bulk',),
'allocate': { '_path': ( 'allocate',
'ecoli-protein-degradation'),
'metabolites': ('bulk',),
'proteins': ('bulk',)}},
'ecoli-chromosome-replication_requester': { 'replisome_trimers': ('bulk',),
'replisome_monomers': ('bulk',),
'dntps': ('bulk',),
'ppi': ('bulk',),
'active_replisomes': ( 'unique',
'active_replisome'),
'oriCs': ('unique', 'oriC'),
'chromosome_domains': ( 'unique',
'chromosome_domain'),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'listeners': ('listeners',),
'environment': ('environment',),
'request': { '_path': ( 'request',
'ecoli-chromosome-replication'),
'replisome_trimers': ( 'bulk',),
'replisome_monomers': ( 'bulk',),
'dntps': ('bulk',),
'ppi': ('bulk',)}},
'ecoli-chromosome-replication_evolver': { 'replisome_trimers': ('bulk',),
'replisome_monomers': ('bulk',),
'dntps': ('bulk',),
'ppi': ('bulk',),
'active_replisomes': ( 'unique',
'active_replisome'),
'oriCs': ('unique', 'oriC'),
'chromosome_domains': ( 'unique',
'chromosome_domain'),
'full_chromosomes': ( 'unique',
'full_chromosome'),
'listeners': ('listeners',),
'environment': ('environment',),
'allocate': { '_path': ( 'allocate',
'ecoli-chromosome-replication'),
'replisome_trimers': ( 'bulk',),
'replisome_monomers': ( 'bulk',),
'dntps': ('bulk',),
'ppi': ('bulk',)}},
'ecoli-mass-listener': { 'bulk': ('bulk',),
'unique': ('unique',),
'listeners': ('listeners',)},
'mRNA_counts_listener': { 'listeners': ('listeners',),
'RNAs': ('unique', 'RNA')},
'allocator': { 'request': ('request',),
'allocate': ('allocate',),
'bulk': ('bulk',)}}
plot the topology
[13]:
ecoli_master_composite = Composite({
'processes': sim_master.ecoli.processes,
'topology': sim_master.ecoli.topology,
})
topology_settings = get_ecoli_partition_topology_settings()
fig = plot_topology(ecoli_master_composite, topology_settings)
run simulation
[14]:
sim_master.run()
master_output = sim_master.query()
Simulation ID: 72a05148-2d74-11ec-947e-acde48001122
Created: 10/14/2021 at 21:57:53
Completed in 141.15 seconds
Mass Fraction Summary Plot
[30]:
from ecoli.analysis.massFractionSummary import Plot as massFractionPlot
fig = massFractionPlot(master_output).do_plot(master_output)
fig
[30]:
