ecoli

• ecoli.analysis
  • ecoli.analysis.antibiotics_colony
    • ecoli.analysis.antibiotics_colony.amp_plots
    • ecoli.analysis.antibiotics_colony.exploration
    • ecoli.analysis.antibiotics_colony.load_data
    • ecoli.analysis.antibiotics_colony.metrics
    • ecoli.analysis.antibiotics_colony.plot
    • ecoli.analysis.antibiotics_colony.plot_utils
    • ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot
    • ecoli.analysis.antibiotics_colony.spatial_correlation
    • ecoli.analysis.antibiotics_colony.tet_dry_mass
    • ecoli.analysis.antibiotics_colony.timeseries
    • ecoli.analysis.antibiotics_colony.validation
  • ecoli.analysis.causality_network
    • ecoli.analysis.causality_network.buildCausalityNetwork
    • ecoli.analysis.causality_network.build_network
    • ecoli.analysis.causality_network.network_components
    • ecoli.analysis.causality_network.read_dynamics
  • ecoli.analysis.colony
    • ecoli.analysis.colony.snapshots
  • ecoli.analysis.multidaughter
  • ecoli.analysis.multiexperiment
  • ecoli.analysis.multigeneration
    • ecoli.analysis.multigeneration.new_gene_counts
  • ecoli.analysis.multiseed
    • ecoli.analysis.multiseed.ecocyc_table
    • ecoli.analysis.multiseed.subgenerational_expression_table
  • ecoli.analysis.multivariant
    • ecoli.analysis.multivariant.average_monomer_counts
    • ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps
  • ecoli.analysis.single
    • ecoli.analysis.single.blame
    • ecoli.analysis.single.mass_fraction_summary
• ecoli.composites
  • ecoli.composites.ecoli_configs
  • ecoli.composites.environment
    • ecoli.composites.environment.grow_divide
    • ecoli.composites.environment.lattice
  • ecoli.composites.chemotaxis_minimal
  • ecoli.composites.ecoli_master
  • ecoli.composites.ecoli_master_tests
  • ecoli.composites.ecoli_spatial
• ecoli.experiments
  • ecoli.experiments.antibiotics_tests
  • ecoli.experiments.ecoli_engine_process
  • ecoli.experiments.ecoli_master_sim
  • ecoli.experiments.glt_division
  • ecoli.experiments.metabolism_exchanger
  • ecoli.experiments.metabolism_redux_sim
  • ecoli.experiments.tet_amp_sim
• ecoli.library
  • ecoli.library.cell_wall
    • ecoli.library.cell_wall.column_sampler
    • ecoli.library.cell_wall.fit_lysis_time
    • ecoli.library.cell_wall.hole_detection
    • ecoli.library.cell_wall.lattice
  • ecoli.library.create_timeline
  • ecoli.library.data_predicates
  • ecoli.library.initial_conditions
  • ecoli.library.json_state
  • ecoli.library.kinetic_rate_laws
  • ecoli.library.lattice_utils
  • ecoli.library.logging_tools
  • ecoli.library.parameters
  • ecoli.library.parquet_emitter
  • ecoli.library.pymunk_multibody
  • ecoli.library.schema
  • ecoli.library.serialize
  • ecoli.library.sim_data
  • ecoli.library.units
  • ecoli.library.updaters
• ecoli.processes
  • ecoli.processes.chemotaxis
    • ecoli.processes.chemotaxis.chemoreceptor_cluster
    • ecoli.processes.chemotaxis.coarse_motor
    • ecoli.processes.chemotaxis.flagella_motor
  • ecoli.processes.environment
    • ecoli.processes.environment.derive_globals
    • ecoli.processes.environment.diffusion_field
    • ecoli.processes.environment.exchange
    • ecoli.processes.environment.exchange_data
    • ecoli.processes.environment.field_timeline
    • ecoli.processes.environment.local_field
    • ecoli.processes.environment.lysis
    • ecoli.processes.environment.media_update
    • ecoli.processes.environment.multibody_physics
    • ecoli.processes.environment.reaction_diffusion_field
  • ecoli.processes.listeners
    • ecoli.processes.listeners.RNA_counts
    • ecoli.processes.listeners.aggregator
    • ecoli.processes.listeners.dna_supercoiling
    • ecoli.processes.listeners.mass_listener
    • ecoli.processes.listeners.monomer_counts
    • ecoli.processes.listeners.replication_data
    • ecoli.processes.listeners.ribosome_data
    • ecoli.processes.listeners.rna_synth_prob
    • ecoli.processes.listeners.rnap_data
    • ecoli.processes.listeners.unique_molecule_counts
  • ecoli.processes.membrane
    • ecoli.processes.membrane.membrane_potential
  • ecoli.processes.spatiality
    • ecoli.processes.spatiality.diffusion_network
    • ecoli.processes.spatiality.spatial_geometry
  • ecoli.processes.stubs
    • ecoli.processes.stubs.exchange_stub
    • ecoli.processes.stubs.exchanger_stub
  • ecoli.processes.allocator
  • ecoli.processes.bulk_timeline
  • ecoli.processes.cell_division
  • ecoli.processes.chemostat
  • ecoli.processes.chromosome_replication
  • ecoli.processes.chromosome_structure
  • ecoli.processes.complexation
  • ecoli.processes.concentrations_deriver
  • ecoli.processes.division_detector
  • ecoli.processes.engine_process
  • ecoli.processes.enzyme_kinetics
  • ecoli.processes.equilibrium
  • ecoli.processes.global_clock
  • ecoli.processes.metabolism
  • ecoli.processes.metabolism_redux
  • ecoli.processes.metabolism_redux_classic
  • ecoli.processes.partition
  • ecoli.processes.polypeptide_elongation
  • ecoli.processes.polypeptide_initiation
  • ecoli.processes.protein_degradation
  • ecoli.processes.registries
  • ecoli.processes.rna_degradation
  • ecoli.processes.rna_interference
  • ecoli.processes.rna_maturation
  • ecoli.processes.shape
  • ecoli.processes.tf_binding
  • ecoli.processes.tf_unbinding
  • ecoli.processes.transcript_elongation
  • ecoli.processes.transcript_initiation
  • ecoli.processes.two_component_system
  • ecoli.processes.unique_update
• ecoli.variants
  • ecoli.variants.condition
  • ecoli.variants.new_gene_internal_shift
  • ecoli.variants.variant_test