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A
ABM
absolute_position() (vivarium.library.polymerize.Template method)
add_arguments() (in module vivarium.experiments.chemotaxis)
(vivarium.library.rate_law_utilities.RateLawUtilities method)
add_barriers() (vivarium.library.pymunk_multibody.PymunkMultibody method)
add_body_from_center() (vivarium.library.pymunk_multibody.PymunkMultibody method)
add_connection_args() (vivarium.analysis.analyze.Analyzer static method)
add_media() (vivarium.library.make_media.Media method)
add_merge() (in module vivarium.library.polymerize)
AddIngredientsError
advance_replisomes() (vivarium.states.chromosome.Chromosome method)
Agent-Based Model
Agent-Based Models
agent_body_config() (in module vivarium.processes.multibody_physics)
agent_environment_experiment() (in module vivarium.core.composition)
agent_parser() (in module vivarium.experiments.chemotaxis)
agent_timeseries_from_data() (in module vivarium.core.composition)
agent_type() (in module vivarium.experiments.chemotaxis)
all_products() (in module vivarium.library.polymerize)
all_subkeys() (in module vivarium.processes.degradation)
always_true() (in module vivarium.core.experiment)
amino_acid_records (in module vivarium.data.amino_acids)
amino_acids (in module vivarium.data.amino_acids)
analyze_rate_laws() (in module vivarium.library.rate_law_utilities)
analyze_transport_metabolism() (in module vivarium.compartments.transport_metabolism)
Analyzer (class in vivarium.analysis.analyze)
animate_frame() (vivarium.processes.cellular_potts.CellularPotts method)
(vivarium.processes.multibody_physics.Multibody method)
AntibioticDetector (class in vivarium.processes.death)
Antibiotics (class in vivarium.compartments.antibiotics)
AntibioticTransport (class in vivarium.processes.antibiotic_transport)
apply_config() (vivarium.core.experiment.Store method)
apply_defaults() (vivarium.core.experiment.Store method)
apply_jitter_force() (vivarium.library.pymunk_multibody.PymunkMultibody method)
apply_motile_force() (vivarium.library.pymunk_multibody.PymunkMultibody method)
apply_subschema() (vivarium.core.experiment.Store method)
apply_subschema_config() (vivarium.core.experiment.Store method)
apply_subschemas() (vivarium.core.experiment.Store method)
apply_thresholds() (vivarium.states.chromosome.Chromosome method)
apply_update() (vivarium.core.experiment.Experiment method)
(vivarium.core.experiment.Store method)
apply_viscous_force() (vivarium.library.pymunk_multibody.PymunkMultibody method)
AREA (vivarium.processes.derive_colony_shape.Variables attribute)
AREA_PATH (in module vivarium.plots.colonies)
array_to_list() (in module vivarium.data.spreadsheets)
assert_timeseries_close() (in module vivarium.core.composition)
assert_timeseries_correlated() (in module vivarium.core.composition)
assoc_in() (in module vivarium.core.process)
assoc_path() (in module vivarium.core.experiment)
AXIS_RATIO_PATH (in module vivarium.plots.colonies)
B
between() (vivarium.library.polymerize.Terminator method)
bind() (vivarium.library.polymerize.Polymerase method)
bind_rnap() (vivarium.states.chromosome.Chromosome method)
binding_state() (vivarium.library.polymerize.Template method)
BindingSite (class in vivarium.library.polymerize)
boltzmann_acceptance_function() (vivarium.processes.cellular_potts.CPM method)
Boundary Store
Boundary Stores
build_affinity_vector() (vivarium.processes.transcription.Transcription method)
build_complexation_stoichiometry() (in module vivarium.processes.complexation)
build_double_rates() (in module vivarium.library.polymerize)
build_double_stoichiometry() (in module vivarium.library.polymerize)
build_model() (in module vivarium.library.cobra_fba)
build_rule() (in module vivarium.library.regulation_logic)
build_stoichiometry() (in module vivarium.library.polymerize)
C
calc_shape_metrics() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
calculate_mass() (in module vivarium.processes.tree_mass)
CellularPotts (class in vivarium.processes.cellular_potts)
check_can_survive() (vivarium.processes.death.AntibioticDetector method)
(vivarium.processes.death.DetectorInterface method)
check_default() (vivarium.core.experiment.Store method)
check_in_set() (in module vivarium.processes.diffusion_network)
check_path_exists() (in module vivarium.parameters.parameters)
check_plt_backend() (in module vivarium.plots.multibody_physics)
check_value() (vivarium.core.experiment.Store method)
ChemotaxisExpressionFlagella (class in vivarium.compartments.chemotaxis_flagella)
ChemotaxisMaster (class in vivarium.compartments.chemotaxis_master)
ChemotaxisMinimal (class in vivarium.compartments.chemotaxis_minimal)
ChemotaxisODEExpressionFlagella (class in vivarium.compartments.chemotaxis_flagella)
ChemotaxisVariableFlagella (class in vivarium.compartments.chemotaxis_flagella)
choose_element() (in module vivarium.processes.transcription)
choose_product() (vivarium.library.polymerize.Template method)
choose_terminator() (vivarium.library.polymerize.Template method)
Chromosome (class in vivarium.states.chromosome)
chromosome_config() (vivarium.processes.transcription.Transcription method)
CIRCUMFERENCE (vivarium.processes.derive_colony_shape.Variables attribute)
CIRCUMFERENCE_AREA_RATIO_PATH (in module vivarium.plots.colonies)
CIRCUMFERENCE_PATH (in module vivarium.plots.colonies)
client (vivarium.core.emitter.DatabaseEmitter attribute)
cmp() (in module vivarium.library.make_media)
cobra_configuration (vivarium.library.cobra_fba.CobraFBA attribute)
CobraFBA (class in vivarium.library.cobra_fba)
cofactor_denominator() (in module vivarium.library.kinetic_rate_laws)
cofactor_numerator() (in module vivarium.library.kinetic_rate_laws)
collapse_network() (in module vivarium.library.make_network)
ColonyShapeDeriver (class in vivarium.processes.derive_colony_shape)
color_phylogeny() (in module vivarium.plots.multibody_physics)
combine_media() (vivarium.library.make_media.Media method)
combine_state() (vivarium.states.chromosome.Chromosome method)
compare() (in module vivarium.library.regulation_logic)
Compartment
compartment_in_experiment() (in module vivarium.core.composition)
Compartments
complete() (vivarium.library.polymerize.Elongation method)
(vivarium.library.polymerize.Polymerase method)
Complexation (class in vivarium.processes.complexation)
concatenate_sequences() (vivarium.data.knowledge_base.KnowledgeBase method)
configure() (vivarium.library.pymunk_multibody.NullScreen method)
configure_emitter() (in module vivarium.core.emitter)
constrain_flux() (vivarium.library.cobra_fba.CobraFBA method)
constrain_reaction_bounds() (vivarium.library.cobra_fba.CobraFBA method)
construct_convenience_rate_law() (in module vivarium.library.kinetic_rate_laws)
contains() (vivarium.states.chromosome.Domain method)
ConvenienceKinetics (class in vivarium.processes.convenience_kinetics)
convert_number() (in module vivarium.library.regulation_logic)
copy_number() (vivarium.states.chromosome.Chromosome method)
corner_from_center() (in module vivarium.library.pymunk_multibody)
count_to_concentration() (vivarium.processes.diffusion_field.DiffusionField method)
counts_to_millimolar() (in module vivarium.library.flux_conversion)
counts_to_molar() (in module vivarium.library.flux_conversion)
CPM (class in vivarium.processes.cellular_potts)
create_indexes() (in module vivarium.core.emitter)
D
d (vivarium.core.experiment.TestUpdateIn attribute)
data_from_database() (in module vivarium.core.emitter)
DatabaseEmitter (class in vivarium.core.emitter)
DataStore (class in vivarium.data.knowledge_base)
Datum (class in vivarium.library.datum)
daughter_locations() (in module vivarium.processes.multibody_physics)
daughter_phylogeny_id() (in module vivarium.processes.meta_division)
daughter_uuid() (in module vivarium.processes.meta_division)
DeathFreezeState (class in vivarium.processes.death)
deep_merge() (in module vivarium.library.dict_utils)
deep_merge_check() (in module vivarium.library.dict_utils)
deep_merge_combine_lists() (in module vivarium.library.dict_utils)
default_expression_config() (in module vivarium.compartments.transport_metabolism)
default_host (vivarium.core.emitter.DatabaseEmitter attribute)
default_metabolism_config() (in module vivarium.compartments.flagella_expression)
(in module vivarium.compartments.master)
(in module vivarium.compartments.transport_metabolism)
default_state() (vivarium.core.process.Process method)
default_transport_config() (in module vivarium.compartments.transport_metabolism)
defaults (vivarium.compartments.antibiotics.Antibiotics attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisVariableFlagella attribute)
(vivarium.compartments.chemotaxis_master.ChemotaxisMaster attribute)
(vivarium.compartments.chemotaxis_minimal.ChemotaxisMinimal attribute)
(vivarium.compartments.flagella_expression.FlagellaExpressionMetabolism attribute)
(vivarium.compartments.gene_expression.GeneExpression attribute)
(vivarium.compartments.growth_division.GrowthDivision attribute)
(vivarium.compartments.growth_division_minimal.GrowthDivisionMinimal attribute)
(vivarium.compartments.injected_glc_phosphorylation.InjectedGlcPhosphorylation attribute)
(vivarium.compartments.lattice.Lattice attribute)
(vivarium.compartments.master.Master attribute)
(vivarium.compartments.static_lattice.StaticLattice attribute)
(vivarium.compartments.transport_metabolism.TransportMetabolism attribute)
(vivarium.core.experiment.Electron attribute)
(vivarium.core.experiment.Proton attribute)
(vivarium.core.experiment.Sine attribute)
(vivarium.core.process.Generator attribute)
(vivarium.core.process.Process attribute)
(vivarium.data.proteins.Protein attribute)
(vivarium.library.datum.Datum attribute)
(vivarium.library.polymerize.BindingSite attribute)
(vivarium.library.polymerize.Polymerase attribute)
(vivarium.library.polymerize.Template attribute)
(vivarium.library.polymerize.Terminator attribute)
(vivarium.library.pymunk_multibody.PymunkMultibody attribute)
(vivarium.parameters.parameters.TestConvienceKinetics attribute)
(vivarium.processes.antibiotic_transport.AntibioticTransport attribute)
(vivarium.processes.cellular_potts.CellularPotts attribute)
(vivarium.processes.complexation.Complexation attribute)
(vivarium.processes.convenience_kinetics.ConvenienceKinetics attribute)
(vivarium.processes.degradation.RnaDegradation attribute)
(vivarium.processes.derive_colony_shape.ColonyShapeDeriver attribute)
(vivarium.processes.derive_concentrations.DeriveConcentrations attribute)
(vivarium.processes.derive_counts.DeriveCounts attribute)
(vivarium.processes.derive_globals.DeriveGlobals attribute)
(vivarium.processes.diffusion_field.DiffusionField attribute)
(vivarium.processes.diffusion_network.DiffusionNetwork attribute)
(vivarium.processes.division_volume.DivisionVolume attribute)
(vivarium.processes.glucose_phosphorylation.GlucosePhosphorylation attribute)
(vivarium.processes.growth.Growth attribute)
(vivarium.processes.growth_protein.GrowthProtein attribute)
(vivarium.processes.Kremling2007_transport.Transport attribute)
(vivarium.processes.membrane_potential.MembranePotential attribute)
(vivarium.processes.meta_division.MetaDivision attribute)
(vivarium.processes.metabolism.Metabolism attribute)
(vivarium.processes.minimal_expression.MinimalExpression attribute)
(vivarium.processes.multibody_physics.Multibody attribute)
(vivarium.processes.nonspatial_environment.NonSpatialEnvironment attribute)
(vivarium.processes.ode_expression.ODE_expression attribute)
(vivarium.processes.static_field.StaticField attribute)
(vivarium.processes.template_process.Template attribute)
(vivarium.processes.timeline.TimelineProcess attribute)
(vivarium.processes.transcription.Transcription attribute)
(vivarium.processes.translation.Translation attribute)
(vivarium.processes.tree_mass.TreeMass attribute)
(vivarium.states.chromosome.Chromosome attribute)
(vivarium.states.chromosome.Domain attribute)
(vivarium.states.chromosome.Operon attribute)
(vivarium.states.chromosome.Rnap attribute)
Defer (class in vivarium.core.experiment)
degradation_sequences() (in module vivarium.compartments.gfp_expression)
delete_path() (vivarium.core.experiment.Store method)
delivery_report() (in module vivarium.core.emitter)
depth() (vivarium.core.experiment.Store method)
derive_defaults() (vivarium.core.process.Process method)
DeriveConcentrations (class in vivarium.processes.derive_concentrations)
DeriveCounts (class in vivarium.processes.derive_counts)
DeriveGlobals (class in vivarium.processes.derive_globals)
Deriver
(class in vivarium.core.process)
Derivers
derivers() (vivarium.core.process.Process method)
(vivarium.processes.complexation.Complexation method)
(vivarium.processes.convenience_kinetics.ConvenienceKinetics method)
(vivarium.processes.degradation.RnaDegradation method)
(vivarium.processes.glucose_phosphorylation.GlucosePhosphorylation method)
(vivarium.processes.growth.Growth method)
(vivarium.processes.growth_protein.GrowthProtein method)
(vivarium.processes.metabolism.Metabolism method)
(vivarium.processes.minimal_expression.MinimalExpression method)
(vivarium.processes.ode_expression.ODE_expression method)
(vivarium.processes.template_process.Template method)
(vivarium.processes.transcription.Transcription method)
(vivarium.processes.translation.Translation method)
descendants() (vivarium.states.chromosome.Domain method)
DETECTOR_CLASSES (in module vivarium.processes.death)
DetectorInterface (class in vivarium.processes.death)
diffuse() (vivarium.processes.diffusion_field.DiffusionField method)
diffusion_delta() (vivarium.processes.diffusion_field.DiffusionField method)
(vivarium.processes.diffusion_network.DiffusionNetwork method)
DiffusionField (class in vivarium.processes.diffusion_field)
DiffusionNetwork (class in vivarium.processes.diffusion_network)
dissoc() (in module vivarium.core.experiment)
divide_chromosome() (vivarium.states.chromosome.Chromosome method)
divide_value() (vivarium.core.experiment.Store method)
Divider
divider_set_false() (in module vivarium.processes.meta_division)
Dividers
DivisionVolume (class in vivarium.processes.division_volume)
Domain (class in vivarium.states.chromosome)
E
ecoli_sequence (vivarium.data.chromosomes.flagella_chromosome.FlagellaChromosome attribute)
effective_energy() (vivarium.processes.cellular_potts.CPM method)
Electron (class in vivarium.core.experiment)
elongate_to() (vivarium.library.polymerize.Elongation method)
Elongation (class in vivarium.library.polymerize)
Embedded Timeseries
emit() (vivarium.core.emitter.DatabaseEmitter method)
(vivarium.core.emitter.Emitter method)
(vivarium.core.emitter.KafkaEmitter method)
(vivarium.core.emitter.NullEmitter method)
(vivarium.core.emitter.TimeSeriesEmitter method)
emit_configuration() (vivarium.core.experiment.Experiment method)
emit_data() (vivarium.core.experiment.Experiment method)
(vivarium.core.experiment.Store method)
emit_environment_config() (in module vivarium.core.emitter)
Emitter
(class in vivarium.core.emitter)
Emitters
end() (vivarium.core.experiment.Experiment method)
(vivarium.core.process.ParallelProcess method)
energy_synthesis_plot() (in module vivarium.plots.metabolism)
establish_path() (vivarium.core.experiment.Store method)
evaluate_compare() (in module vivarium.library.regulation_logic)
evaluate_group() (in module vivarium.library.regulation_logic)
evaluate_logic() (in module vivarium.library.regulation_logic)
evaluate_rule() (in module vivarium.library.regulation_logic)
evaluate_symbol() (in module vivarium.library.regulation_logic)
evaluate_term() (in module vivarium.library.regulation_logic)
evaluate_tuple_key() (in module vivarium.library.regulation_logic)
Exchange
Exchanges
Experiment
(class in vivarium.core.experiment)
Experiments
external_reactions() (vivarium.library.cobra_fba.CobraFBA method)
extract_model() (in module vivarium.library.cobra_fba)
F
field_from_locations_series() (in module vivarium.processes.diffusion_network)
fields() (vivarium.library.datum.Datum method)
first() (in module vivarium.library.datum)
first_value() (in module vivarium.library.datum)
flagella_expression_compartment() (in module vivarium.compartments.flagella_expression)
FlagellaChromosome (class in vivarium.data.chromosomes.flagella_chromosome)
FlagellaExpressionMetabolism (class in vivarium.compartments.flagella_expression)
flatten() (in module vivarium.library.polymerize)
(vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
flatten_port_dicts() (in module vivarium.library.dict_utils)
flatten_timeseries() (in module vivarium.library.dict_utils)
flux_to_counts() (vivarium.processes.transport_lookup.TransportLookup method)
format_data_for_colony_metrics() (vivarium.analysis.analyze.Analyzer static method)
format_data_for_snapshots() (vivarium.analysis.analyze.Analyzer static method)
format_data_for_tags() (vivarium.analysis.analyze.Analyzer static method)
format_dict() (in module vivarium.library.pretty)
frequencies() (in module vivarium.states.chromosome)
front_from_corner() (in module vivarium.library.pymunk_multibody)
G
gather_genes() (in module vivarium.processes.translation)
gaussian() (in module vivarium.processes.diffusion_field)
gen_agent_colony_map() (in module vivarium.processes.derive_colony_shape)
gene_network_plot() (in module vivarium.compartments.gene_expression)
GeneExpression (class in vivarium.compartments.gene_expression)
generate() (vivarium.core.experiment.Store method)
(vivarium.core.process.Generator method)
generate_derivers() (in module vivarium.core.process)
generate_gfp_compartment() (in module vivarium.compartments.gfp_expression)
generate_paths() (vivarium.core.experiment.Store method)
generate_processes() (vivarium.compartments.antibiotics.Antibiotics method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisVariableFlagella method)
(vivarium.compartments.chemotaxis_master.ChemotaxisMaster method)
(vivarium.compartments.chemotaxis_minimal.ChemotaxisMinimal method)
(vivarium.compartments.flagella_expression.FlagellaExpressionMetabolism method)
(vivarium.compartments.gene_expression.GeneExpression method)
(vivarium.compartments.growth_division.GrowthDivision method)
(vivarium.compartments.growth_division_minimal.GrowthDivisionMinimal method)
(vivarium.compartments.injected_glc_phosphorylation.InjectedGlcPhosphorylation method)
(vivarium.compartments.lattice.Lattice method)
(vivarium.compartments.master.Master method)
(vivarium.compartments.static_lattice.StaticLattice method)
(vivarium.compartments.transport_metabolism.TransportMetabolism method)
(vivarium.core.composition.ToyCompartment method)
(vivarium.core.process.Generator method)
(vivarium.core.process.Process method)
(vivarium.parameters.parameters.TestConvienceKinetics method)
(vivarium.processes.death.ToyDeath method)
generate_state() (in module vivarium.core.experiment)
generate_template() (in module vivarium.library.polymerize)
generate_topology() (vivarium.compartments.antibiotics.Antibiotics method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella method)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisVariableFlagella method)
(vivarium.compartments.chemotaxis_master.ChemotaxisMaster method)
(vivarium.compartments.chemotaxis_minimal.ChemotaxisMinimal method)
(vivarium.compartments.flagella_expression.FlagellaExpressionMetabolism method)
(vivarium.compartments.gene_expression.GeneExpression method)
(vivarium.compartments.growth_division.GrowthDivision method)
(vivarium.compartments.growth_division_minimal.GrowthDivisionMinimal method)
(vivarium.compartments.injected_glc_phosphorylation.InjectedGlcPhosphorylation method)
(vivarium.compartments.lattice.Lattice method)
(vivarium.compartments.master.Master method)
(vivarium.compartments.static_lattice.StaticLattice method)
(vivarium.compartments.transport_metabolism.TransportMetabolism method)
(vivarium.core.composition.ToyCompartment method)
(vivarium.core.process.Generator method)
(vivarium.core.process.Process method)
(vivarium.parameters.parameters.TestConvienceKinetics method)
(vivarium.processes.death.ToyDeath method)
Generator (class in vivarium.core.process)
generic_visit() (vivarium.library.make_media.RecipeConstructor method)
get() (vivarium.core.experiment.Defer method)
(vivarium.core.experiment.InvokeProcess method)
(vivarium.core.process.ParallelProcess method)
(vivarium.processes.multibody_physics.InvokeUpdate method)
get_agent_area() (vivarium.processes.cellular_potts.CPM method)
get_agent_trajectories() (in module vivarium.plots.multibody_physics)
get_agent_type_colors() (in module vivarium.plots.multibody_physics)
get_agents_areas() (vivarium.processes.cellular_potts.CPM method)
get_atlas_client() (in module vivarium.core.emitter)
get_atlas_database_emitter_config() (in module vivarium.core.emitter)
get_baseline_config() (in module vivarium.compartments.chemotaxis_flagella)
(in module vivarium.processes.multibody_physics)
get_bin_site() (vivarium.processes.diffusion_field.DiffusionField method)
get_body_position() (vivarium.library.pymunk_multibody.PymunkMultibody method)
get_body_positions() (vivarium.library.pymunk_multibody.PymunkMultibody method)
get_chemotaxis_config() (in module vivarium.compartments.chemotaxis_minimal)
get_concentration() (vivarium.processes.static_field.StaticField method)
get_config() (vivarium.core.experiment.Store method)
get_cpm_config() (in module vivarium.processes.cellular_potts)
get_cpm_minimum_config() (in module vivarium.processes.cellular_potts)
get_data() (vivarium.analysis.analyze.Analyzer static method)
(vivarium.core.emitter.DatabaseEmitter method)
(vivarium.core.emitter.Emitter method)
(vivarium.core.emitter.TimeSeriesEmitter method)
get_default_global_state() (in module vivarium.processes.derive_globals)
get_e_coli_core_config() (in module vivarium.processes.metabolism)
get_emitter() (in module vivarium.core.emitter)
get_exponential_config() (in module vivarium.processes.diffusion_field)
(in module vivarium.processes.static_field)
get_exponential_env_config() (in module vivarium.experiments.chemotaxis)
get_fg_from_counts() (in module vivarium.processes.metabolism)
get_flagella_expression() (in module vivarium.processes.ode_expression)
get_flagella_expression_config() (in module vivarium.compartments.flagella_expression)
get_flagella_initial_state() (in module vivarium.compartments.flagella_expression)
get_flagella_metabolism_initial_state() (in module vivarium.compartments.flagella_expression)
get_fluorescent_color() (in module vivarium.plots.multibody_physics)
get_fluxes() (vivarium.library.kinetic_rate_laws.KineticFluxModel method)
get_force_with_angle() (in module vivarium.library.pymunk_multibody)
get_gaussian_config() (in module vivarium.processes.diffusion_field)
get_glc_lct_config() (in module vivarium.processes.convenience_kinetics)
get_glc_lct_transport() (in module vivarium.processes.convenience_kinetics)
get_grid_config() (in module vivarium.processes.diffusion_network)
get_history_data_db() (in module vivarium.core.emitter)
get_iAF1260b_config() (in module vivarium.processes.metabolism)
get_in() (in module vivarium.core.experiment)
(vivarium.core.experiment.Store method)
get_inertia() (vivarium.library.pymunk_multibody.PymunkMultibody method)
get_interactions() (vivarium.processes.cellular_potts.CPM method)
get_lacy_config() (in module vivarium.processes.ode_expression)
get_lattice_config() (in module vivarium.compartments.lattice)
get_linear_env_config() (in module vivarium.experiments.chemotaxis)
get_local_client() (in module vivarium.core.emitter)
get_local_environments() (vivarium.processes.diffusion_field.DiffusionField method)
get_loose_nodes() (in module vivarium.library.make_network)
get_metabolism_initial_state() (in module vivarium.compartments.transport_metabolism)
get_molecules() (in module vivarium.library.kinetic_rate_laws)
get_molecules_from_reactions() (in module vivarium.library.rate_law_utilities)
get_mother_machine_config() (in module vivarium.experiments.mother_machine)
get_nested() (in module vivarium.parameters.parameters)
get_parameter_template() (vivarium.library.rate_law_utilities.RateLawUtilities method)
get_parameters() (vivarium.core.process.Generator method)
get_parameters_logspace() (in module vivarium.parameters.parameters)
get_path() (vivarium.core.experiment.Store method)
get_path_list_from_dict() (in module vivarium.library.dict_utils)
get_path_timeseries() (vivarium.core.emitter.Emitter method)
get_paths() (vivarium.core.experiment.Store method)
get_phylogeny_colors_from_names() (in module vivarium.plots.multibody_physics)
get_random_field_config() (in module vivarium.processes.diffusion_field)
get_reaction_bounds() (vivarium.library.cobra_fba.CobraFBA method)
get_reactions() (in module vivarium.library.make_network)
(vivarium.library.cobra_fba.CobraFBA method)
get_reactions_from_exchange() (in module vivarium.library.rate_law_utilities)
get_saved_media() (vivarium.library.make_media.Media method)
get_schema() (vivarium.core.process.Process method)
get_secretion_agent_config() (in module vivarium.processes.diffusion_field)
get_shape() (vivarium.library.pymunk_multibody.PymunkMultibody method)
get_single_local_environments() (vivarium.processes.diffusion_field.DiffusionField method)
get_static_lattice_config() (in module vivarium.compartments.static_lattice)
get_synonym() (in module vivarium.data.synonyms)
get_template() (vivarium.core.experiment.Store method)
get_timeline() (in module vivarium.compartments.chemotaxis_flagella)
get_timeseries() (vivarium.core.emitter.Emitter method)
get_toy_config() (in module vivarium.processes.convenience_kinetics)
get_toy_configuration() (in module vivarium.processes.metabolism)
get_toy_expression_config() (in module vivarium.processes.minimal_expression)
get_two_compartment_config() (in module vivarium.processes.diffusion_network)
get_updater() (vivarium.core.experiment.Store method)
get_value() (vivarium.core.experiment.Store method)
get_value_from_path() (in module vivarium.library.dict_utils)
get_values() (vivarium.core.experiment.Store method)
glucose_phosphorylation_experiment() (in module vivarium.experiments.glucose_phosphorylation)
GlucosePhosphorylation (class in vivarium.processes.glucose_phosphorylation)
group() (in module vivarium.library.regulation_logic)
Growth (class in vivarium.processes.growth)
growth_rate (vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
GROWTH_RATE (vivarium.core.composition.ToyLinearGrowthDeathProcess attribute)
GrowthDivision (class in vivarium.compartments.growth_division)
GrowthDivisionMinimal (class in vivarium.compartments.growth_division_minimal)
GrowthProtein (class in vivarium.processes.growth_protein)
H
Hierarchies
Hierarchy
I
identity() (in module vivarium.core.experiment)
init_axes() (in module vivarium.plots.multibody_physics)
initial_ligand (vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
initial_mass (vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
initialize_spatial_figure() (in module vivarium.plots.multibody_physics)
initiate_replication() (vivarium.states.chromosome.Chromosome method)
InjectedGlcPhosphorylation (class in vivarium.compartments.injected_glc_phosphorylation)
Injector (class in vivarium.processes.injector)
inner_value() (vivarium.core.experiment.Store method)
internal_reactions() (vivarium.library.cobra_fba.CobraFBA method)
inverse_kronecker_delta() (vivarium.processes.cellular_potts.CPM method)
inverse_topology() (in module vivarium.core.experiment)
invert_index() (in module vivarium.data.synonyms)
invert_topology() (in module vivarium.core.experiment)
invoke() (vivarium.core.experiment.MultiInvoke method)
invoke_process() (in module vivarium.core.experiment)
(vivarium.core.experiment.Experiment method)
InvokeProcess (class in vivarium.core.experiment)
InvokeUpdate (class in vivarium.processes.multibody_physics)
is_bound() (vivarium.library.polymerize.Polymerase method)
is_complete() (vivarium.library.polymerize.Polymerase method)
is_deriver() (vivarium.core.process.Deriver method)
(vivarium.core.process.Process method)
is_occluding() (vivarium.library.polymerize.Polymerase method)
is_polymerizing() (vivarium.library.polymerize.Polymerase method)
is_unoccluding() (vivarium.library.polymerize.Polymerase method)
J
JsonFBA (class in vivarium.library.cobra_fba)
JsonReader (class in vivarium.data.spreadsheets)
JsonWriter (class in vivarium.data.spreadsheets)
K
KafkaEmitter (class in vivarium.core.emitter)
key_for_value() (in module vivarium.core.experiment)
keys_list() (in module vivarium.library.dict_utils)
KineticFluxModel (class in vivarium.library.kinetic_rate_laws)
kinetics() (in module vivarium.library.polymerize)
(in module vivarium.processes.degradation)
knowledge_base (vivarium.data.chromosomes.flagella_chromosome.FlagellaChromosome attribute)
KnowledgeBase (class in vivarium.data.knowledge_base)
kremling_figures() (in module vivarium.processes.Kremling2007_transport)
L
last_terminator() (vivarium.library.polymerize.Template method)
Lattice (class in vivarium.compartments.lattice)
length_from_volume() (in module vivarium.processes.derive_globals)
ligand_id (vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
LineWidthData (class in vivarium.plots.multibody_physics)
load_data() (vivarium.processes.transport_lookup.TransportLookup method)
load_lookup() (in module vivarium.library.look_up)
load_reactions() (in module vivarium.library.rate_law_utilities)
load_timeseries() (in module vivarium.core.composition)
load_tsv() (in module vivarium.data.spreadsheets)
local_timestep() (vivarium.core.process.Process method)
logic() (in module vivarium.library.regulation_logic)
look_up() (vivarium.library.look_up.LookUp method)
LookUp (class in vivarium.library.look_up)
M
main() (in module vivarium.compartments.antibiotics)
(in module vivarium.compartments.lattice)
(in module vivarium.processes.antibiotic_transport)
(in module vivarium.processes.injector)
MAJOR_AXIS (vivarium.processes.derive_colony_shape.Variables attribute)
MAJOR_AXIS_PATH (in module vivarium.plots.colonies)
major_minor_axes() (in module vivarium.processes.derive_colony_shape)
make_agent_config() (in module vivarium.experiments.chemotaxis)
make_agents() (in module vivarium.core.composition)
make_compartment_topology() (in module vivarium.compartments.flagella_expression)
make_configuration() (in module vivarium.library.kinetic_rate_laws)
make_dir() (in module vivarium.compartments.chemotaxis_flagella)
(in module vivarium.experiments.chemotaxis)
make_experiment_from_compartment_dicts() (in module vivarium.core.composition)
make_experiment_from_configs() (in module vivarium.core.composition)
make_field() (in module vivarium.processes.static_field)
make_flagella_network() (in module vivarium.compartments.flagella_expression)
make_gradient() (in module vivarium.processes.diffusion_field)
make_kinetic_rate() (in module vivarium.processes.metabolism)
make_location_network() (in module vivarium.processes.diffusion_network)
make_network() (in module vivarium.library.make_network)
make_path_dict() (in module vivarium.library.dict_utils)
make_proton() (in module vivarium.core.experiment)
make_random_position() (in module vivarium.processes.multibody_physics)
make_rate_laws() (in module vivarium.library.kinetic_rate_laws)
make_recipe() (vivarium.library.make_media.Media method)
make_str_dict() (in module vivarium.library.dict_utils)
make_timeline() (vivarium.library.make_media.Media method)
mark_deleted() (vivarium.core.experiment.Store method)
Masking
MASS (vivarium.processes.derive_colony_shape.Variables attribute)
Master (class in vivarium.compartments.master)
Media (class in vivarium.library.make_media)
MembranePotential (class in vivarium.processes.membrane_potential)
merge_dicts() (in module vivarium.library.dict_utils)
merge_overrides() (vivarium.core.process.Process method)
merge_subtopology() (vivarium.core.experiment.Store method)
Metabolism (class in vivarium.processes.metabolism)
metabolism_similar_to_reference() (in module vivarium.processes.metabolism)
metabolism_timestep_config() (in module vivarium.compartments.chemotaxis_master)
MetaDivision (class in vivarium.processes.meta_division)
millimolar_to_counts() (in module vivarium.library.flux_conversion)
MinimalExpression (class in vivarium.processes.minimal_expression)
MINOR_AXIS (vivarium.processes.derive_colony_shape.Variables attribute)
MINOR_AXIS_PATH (in module vivarium.plots.colonies)
molar_to_counts() (in module vivarium.library.flux_conversion)
molar_to_molDCWhr() (in module vivarium.library.flux_conversion)
mother_machine_body_config() (in module vivarium.experiments.mother_machine)
mother_machine_experiment() (in module vivarium.experiments.mother_machine)
MSM
Multibody (class in vivarium.processes.multibody_physics)
MultiInvoke (class in vivarium.core.experiment)
Multiscale Model
Multiscale Models
mutate() (vivarium.processes.cellular_potts.CPM method)
mutate_color() (in module vivarium.plots.multibody_physics)
N
n_flagella (vivarium.compartments.chemotaxis_flagella.ChemotaxisExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisODEExpressionFlagella attribute)
(vivarium.compartments.chemotaxis_flagella.ChemotaxisVariableFlagella attribute)
NAME (in module vivarium.processes.convenience_kinetics)
name (vivarium.compartments.antibiotics.Antibiotics attribute)
(vivarium.compartments.flagella_expression.FlagellaExpressionMetabolism attribute)
(vivarium.compartments.transport_metabolism.TransportMetabolism attribute)
(vivarium.core.composition.ToyDeath attribute)
(vivarium.core.composition.ToyDeriveVolume attribute)
(vivarium.core.composition.ToyLinearGrowthDeathProcess attribute)
(vivarium.core.composition.ToyMetabolism attribute)
(vivarium.core.composition.ToyTransport attribute)
(vivarium.core.experiment.Electron attribute)
(vivarium.core.experiment.Proton attribute)
(vivarium.core.experiment.Sine attribute)
(vivarium.processes.antibiotic_transport.AntibioticTransport attribute)
(vivarium.processes.cellular_potts.CellularPotts attribute)
(vivarium.processes.complexation.Complexation attribute)
(vivarium.processes.convenience_kinetics.ConvenienceKinetics attribute)
(vivarium.processes.death.DeathFreezeState attribute)
(vivarium.processes.death.ToyAntibioticInjector attribute)
(vivarium.processes.degradation.RnaDegradation attribute)
(vivarium.processes.derive_colony_shape.ColonyShapeDeriver attribute)
(vivarium.processes.derive_concentrations.DeriveConcentrations attribute)
(vivarium.processes.derive_counts.DeriveCounts attribute)
(vivarium.processes.derive_globals.DeriveGlobals attribute)
(vivarium.processes.diffusion_field.DiffusionField attribute)
(vivarium.processes.diffusion_network.DiffusionNetwork attribute)
(vivarium.processes.division_volume.DivisionVolume attribute)
(vivarium.processes.glucose_phosphorylation.GlucosePhosphorylation attribute)
(vivarium.processes.growth.Growth attribute)
(vivarium.processes.growth_protein.GrowthProtein attribute)
(vivarium.processes.injector.Injector attribute)
(vivarium.processes.Kremling2007_transport.Transport attribute)
(vivarium.processes.membrane_potential.MembranePotential attribute)
(vivarium.processes.meta_division.MetaDivision attribute)
(vivarium.processes.metabolism.Metabolism attribute)
(vivarium.processes.minimal_expression.MinimalExpression attribute)
(vivarium.processes.multibody_physics.Multibody attribute)
(vivarium.processes.nonspatial_environment.NonSpatialEnvironment attribute)
(vivarium.processes.ode_expression.ODE_expression attribute)
(vivarium.processes.static_field.StaticField attribute)
(vivarium.processes.template_process.Template attribute)
(vivarium.processes.timeline.TimelineProcess attribute)
(vivarium.processes.transcription.Transcription attribute)
(vivarium.processes.translation.Translation attribute)
(vivarium.processes.transport_lookup.TransportLookup attribute)
(vivarium.processes.tree_mass.TreeMass attribute)
neighbor_sites() (vivarium.processes.cellular_potts.CPM method)
neighbor_values() (vivarium.processes.cellular_potts.CPM method)
next_polymerize() (vivarium.states.chromosome.Chromosome method)
next_terminator() (vivarium.library.polymerize.Template method)
next_update() (vivarium.core.composition.ToyDeath method)
(vivarium.core.composition.ToyDeriveVolume method)
(vivarium.core.composition.ToyLinearGrowthDeathProcess method)
(vivarium.core.composition.ToyMetabolism method)
(vivarium.core.composition.ToyTransport method)
(vivarium.core.experiment.Electron method)
(vivarium.core.experiment.Proton method)
(vivarium.core.experiment.Sine method)
(vivarium.core.process.Process method)
(vivarium.processes.cellular_potts.CellularPotts method)
(vivarium.processes.complexation.Complexation method)
(vivarium.processes.convenience_kinetics.ConvenienceKinetics method)
(vivarium.processes.death.DeathFreezeState method)
(vivarium.processes.death.ToyAntibioticInjector method)
(vivarium.processes.degradation.RnaDegradation method)
(vivarium.processes.derive_colony_shape.ColonyShapeDeriver method)
(vivarium.processes.derive_concentrations.DeriveConcentrations method)
(vivarium.processes.derive_counts.DeriveCounts method)
(vivarium.processes.derive_globals.DeriveGlobals method)
(vivarium.processes.diffusion_field.DiffusionField method)
(vivarium.processes.diffusion_network.DiffusionNetwork method)
(vivarium.processes.division_volume.DivisionVolume method)
(vivarium.processes.glucose_phosphorylation.GlucosePhosphorylation method)
(vivarium.processes.growth.Growth method)
(vivarium.processes.growth_protein.GrowthProtein method)
(vivarium.processes.injector.Injector method)
(vivarium.processes.Kremling2007_transport.Transport method)
(vivarium.processes.membrane_potential.MembranePotential method)
(vivarium.processes.meta_division.MetaDivision method)
(vivarium.processes.metabolism.Metabolism method)
(vivarium.processes.minimal_expression.MinimalExpression method)
(vivarium.processes.multibody_physics.Multibody method)
(vivarium.processes.nonspatial_environment.NonSpatialEnvironment method)
(vivarium.processes.ode_expression.ODE_expression method)
(vivarium.processes.static_field.StaticField method)
(vivarium.processes.template_process.Template method)
(vivarium.processes.timeline.TimelineProcess method)
(vivarium.processes.transcription.Transcription method)
(vivarium.processes.translation.Translation method)
(vivarium.processes.transport_lookup.TransportLookup method)
(vivarium.processes.tree_mass.TreeMass method)
NoChargeError
NonSpatialEnvironment (class in vivarium.processes.nonspatial_environment)
normalize_path() (in module vivarium.core.experiment)
nucleotides (in module vivarium.data.nucleotides)
NullEmitter (class in vivarium.core.emitter)
NullScreen (class in vivarium.library.pymunk_multibody)
NUM_COLONIES_PATH (in module vivarium.plots.colonies)
number() (in module vivarium.experiments.chemotaxis)
O
objective_value() (vivarium.library.cobra_fba.CobraFBA method)
ODE_expression (class in vivarium.processes.ode_expression)
ones_field() (vivarium.processes.diffusion_field.DiffusionField method)
open_relative() (in module vivarium.library.path)
operator() (in module vivarium.library.regulation_logic)
Operon (class in vivarium.states.chromosome)
operon_from() (vivarium.states.chromosome.RnapTerminator method)
operons() (vivarium.states.chromosome.Chromosome method)
(vivarium.states.chromosome.Promoter method)
optimize() (vivarium.library.cobra_fba.CobraFBA method)
or_default() (vivarium.core.process.Generator method)
(vivarium.core.process.Process method)
order_list_of_paths() (in module vivarium.core.composition)
organize_param_scan_results() (in module vivarium.parameters.parameters)
outer_path() (vivarium.core.experiment.Store method)
override_schemas() (in module vivarium.core.process)
P
ParallelProcess (class in vivarium.core.process)
parameter_scan() (in module vivarium.parameters.parameters)
parse_agents_string() (in module vivarium.experiments.chemotaxis)
Path Timeseries
path_for() (vivarium.core.experiment.Store method)
path_timeseries_from_data() (in module vivarium.core.emitter)
path_timeseries_from_embedded_timeseries() (in module vivarium.core.emitter)
pf() (in module vivarium.core.experiment)
plot() (vivarium.analysis.analyze.Analyzer method)
plot_agent() (in module vivarium.plots.multibody_physics)
plot_agent_trajectory() (in module vivarium.plots.multibody_physics)
plot_agents() (in module vivarium.plots.multibody_physics)
plot_agents_multigen() (in module vivarium.core.composition)
plot_all_state() (in module vivarium.processes.Kremling2007_transport)
plot_chemotaxis_experiment() (in module vivarium.experiments.chemotaxis)
plot_colony_metrics() (in module vivarium.plots.colonies)
(vivarium.analysis.analyze.Analyzer static method)
plot_compartment_topology() (in module vivarium.core.composition)
plot_death_freeze_state_test() (in module vivarium.processes.death)
plot_diauxic_shift() (in module vivarium.plots.transport_metabolism)
plot_diffusion_field_output() (in module vivarium.processes.diffusion_network)
plot_exchanges() (in module vivarium.plots.metabolism)
plot_field() (in module vivarium.processes.static_field)
plot_fields() (in module vivarium.processes.diffusion_field)
plot_gene_expression_output() (in module vivarium.compartments.gene_expression)
plot_metric_across_experiments() (in module vivarium.plots.colonies)
plot_motility() (in module vivarium.plots.multibody_physics)
plot_scan_results() (in module vivarium.parameters.parameters)
plot_simulation_output() (in module vivarium.core.composition)
plot_snapshots() (in module vivarium.plots.multibody_physics)
(vivarium.analysis.analyze.Analyzer static method)
plot_tags() (in module vivarium.plots.multibody_physics)
(vivarium.analysis.analyze.Analyzer static method)
plot_temporal_trajectory() (in module vivarium.plots.multibody_physics)
plot_timeseries() (in module vivarium.compartments.chemotaxis_flagella)
(vivarium.analysis.analyze.Analyzer static method)
Polymerase (class in vivarium.library.polymerize)
polymerize() (vivarium.states.chromosome.Chromosome method)
polymerize_step() (in module vivarium.library.polymerize)
polymerize_to() (in module vivarium.library.polymerize)
Port
Ports
ports() (vivarium.core.process.Process method)
ports_schema() (vivarium.core.composition.ToyDeath method)
(vivarium.core.composition.ToyDeriveVolume method)
(vivarium.core.composition.ToyLinearGrowthDeathProcess method)
(vivarium.core.composition.ToyMetabolism method)
(vivarium.core.composition.ToyTransport method)
(vivarium.core.experiment.Electron method)
(vivarium.core.experiment.Proton method)
(vivarium.core.experiment.Sine method)
(vivarium.core.process.Process method)
(vivarium.processes.cellular_potts.CellularPotts method)
(vivarium.processes.complexation.Complexation method)
(vivarium.processes.convenience_kinetics.ConvenienceKinetics method)
(vivarium.processes.death.DeathFreezeState method)
(vivarium.processes.death.ToyAntibioticInjector method)
(vivarium.processes.degradation.RnaDegradation method)
(vivarium.processes.derive_colony_shape.ColonyShapeDeriver method)
(vivarium.processes.derive_concentrations.DeriveConcentrations method)
(vivarium.processes.derive_counts.DeriveCounts method)
(vivarium.processes.derive_globals.DeriveGlobals method)
(vivarium.processes.diffusion_field.DiffusionField method)
(vivarium.processes.diffusion_network.DiffusionNetwork method)
(vivarium.processes.division_volume.DivisionVolume method)
(vivarium.processes.glucose_phosphorylation.GlucosePhosphorylation method)
(vivarium.processes.growth.Growth method)
(vivarium.processes.growth_protein.GrowthProtein method)
(vivarium.processes.injector.Injector method)
(vivarium.processes.Kremling2007_transport.Transport method)
(vivarium.processes.membrane_potential.MembranePotential method)
(vivarium.processes.meta_division.MetaDivision method)
(vivarium.processes.metabolism.Metabolism method)
(vivarium.processes.minimal_expression.MinimalExpression method)
(vivarium.processes.multibody_physics.Multibody method)
(vivarium.processes.nonspatial_environment.NonSpatialEnvironment method)
(vivarium.processes.ode_expression.ODE_expression method)
(vivarium.processes.static_field.StaticField method)
(vivarium.processes.template_process.Template method)
(vivarium.processes.timeline.TimelineProcess method)
(vivarium.processes.transcription.Transcription method)
(vivarium.processes.translation.Translation method)
(vivarium.processes.transport_lookup.TransportLookup method)
(vivarium.processes.tree_mass.TreeMass method)
position_domains() (vivarium.states.chromosome.Chromosome method)
pp() (in module vivarium.core.experiment)
print_growth() (in module vivarium.compartments.chemotaxis_flagella)
Process
(class in vivarium.core.process)
Process Class
Process Classes
process_in_compartment() (in module vivarium.core.composition)
process_in_experiment() (in module vivarium.core.composition)
process_path_timeseries_for_csv() (in module vivarium.library.timeseries)
process_update() (vivarium.core.experiment.Experiment method)
Processes
processes() (vivarium.core.experiment.Store method)
product_sequences() (vivarium.states.chromosome.Chromosome method)
products() (vivarium.library.polymerize.Template method)
Promoter (class in vivarium.states.chromosome)
promoter_copy_numbers() (vivarium.states.chromosome.Chromosome method)
promoter_domains() (vivarium.states.chromosome.Chromosome method)
promoter_rnaps() (vivarium.states.chromosome.Chromosome method)
Protein (class in vivarium.data.proteins)
Proton (class in vivarium.core.experiment)
pull_data() (vivarium.core.process.Process method)
PymunkMultibody (class in vivarium.library.pymunk_multibody)
R
random_body_position() (in module vivarium.library.pymunk_multibody)
(in module vivarium.processes.multibody_physics)
random_child() (vivarium.states.chromosome.Domain method)
random_neighbor() (vivarium.processes.cellular_potts.CPM method)
random_site() (vivarium.processes.cellular_potts.CPM method)
random_string() (in module vivarium.processes.translation)
rate_laws (vivarium.library.kinetic_rate_laws.KineticFluxModel attribute)
RateLawUtilities (class in vivarium.library.rate_law_utilities)
Raw Data
reaction_ids() (vivarium.library.cobra_fba.CobraFBA method)
read_exchange_fluxes() (vivarium.library.cobra_fba.CobraFBA method)
read_exchange_reactions() (vivarium.library.cobra_fba.CobraFBA method)
read_fluxes() (vivarium.library.cobra_fba.CobraFBA method)
read_internal_fluxes() (vivarium.library.cobra_fba.CobraFBA method)
read_sequence() (in module vivarium.library.fasta)
RecipeConstructor (class in vivarium.library.make_media)
reduce() (vivarium.core.experiment.Store method)
reduce_to() (vivarium.core.experiment.Store method)
regulate_flux() (vivarium.library.cobra_fba.CobraFBA method)
remove_units() (in module vivarium.library.units)
(vivarium.library.make_media.Media method)
RFC
RFC 2119
,
[1]
,
[2]
Ribosome (class in vivarium.processes.translation)
rna_bases() (in module vivarium.states.chromosome)
RnaDegradation (class in vivarium.processes.degradation)
Rnap (class in vivarium.states.chromosome)
RnapTerminator (class in vivarium.states.chromosome)
rotate_agent_series_90() (in module vivarium.plots.multibody_physics)
rotate_bounds_90() (in module vivarium.plots.multibody_physics)
rotate_field_90() (in module vivarium.plots.multibody_physics)
rule() (in module vivarium.experiments.chemotaxis)
(in module vivarium.library.regulation_logic)
rule_parser() (in module vivarium.library.regulation_logic)
run() (vivarium.analysis.analyze.Analyzer method)
(vivarium.library.pymunk_multibody.PymunkMultibody method)
run_analysis() (vivarium.library.rate_law_utilities.RateLawUtilities method)
run_antibiotic_transport() (in module vivarium.processes.antibiotic_transport)
run_antibiotics_composite() (in module vivarium.compartments.antibiotics)
run_chemotaxis_experiment() (in module vivarium.experiments.chemotaxis)
run_chemotaxis_master() (in module vivarium.compartments.chemotaxis_master)
run_chemotaxis_simulation() (in module vivarium.experiments.chemotaxis)
run_compartment_get_output() (in module vivarium.parameters.parameters)
run_CPM() (in module vivarium.processes.cellular_potts)
run_derivers() (vivarium.core.experiment.Experiment method)
run_flagella_compartment() (in module vivarium.compartments.flagella_expression)
run_gene_expression() (in module vivarium.compartments.gene_expression)
run_growth_division() (in module vivarium.processes.multibody_physics)
run_injector() (in module vivarium.processes.injector)
run_jitter() (in module vivarium.processes.multibody_physics)
run_master() (in module vivarium.compartments.master)
run_metabolism() (in module vivarium.processes.metabolism)
run_mother_machine() (in module vivarium.experiments.mother_machine)
run_motility() (in module vivarium.processes.multibody_physics)
run_sim_save_network() (in module vivarium.processes.metabolism)
run_template_process() (in module vivarium.processes.template_process)
run_update() (in module vivarium.core.process)
S
save_flat_timeseries() (in module vivarium.core.composition)
(in module vivarium.library.timeseries)
save_network() (in module vivarium.library.make_network)
save_timeseries() (in module vivarium.core.composition)
scan_conc() (in module vivarium.library.rate_law_utilities)
scan_flagella_expression_parameters() (in module vivarium.compartments.flagella_expression)
scan_test() (in module vivarium.parameters.parameters)
scan_transport_metabolism() (in module vivarium.compartments.transport_metabolism)
Schema
schema (vivarium.library.datum.Datum attribute)
(vivarium.library.polymerize.Template attribute)
(vivarium.states.chromosome.Chromosome attribute)
(vivarium.states.chromosome.Promoter attribute)
Schema Key
Schema Key-Value Pair
Schema Key-Value Pairs
Schema Keys
Schema Value
Schema Values
schema_for() (in module vivarium.core.experiment)
schema_keys (vivarium.core.experiment.Store attribute)
schema_topology() (vivarium.core.experiment.Store method)
Schemas
send_updates() (vivarium.core.experiment.Experiment method)
sequence_monomers() (in module vivarium.states.chromosome)
sequences() (vivarium.states.chromosome.Chromosome method)
serialize_dictionary() (in module vivarium.core.process)
serialize_list() (in module vivarium.core.process)
serialize_value() (in module vivarium.core.process)
set_agent_config() (in module vivarium.experiments.chemotaxis)
set_axes() (in module vivarium.core.composition)
set_environment_config() (in module vivarium.experiments.chemotaxis)
set_exchange_bounds() (vivarium.library.cobra_fba.CobraFBA method)
set_nested() (in module vivarium.parameters.parameters)
set_value() (vivarium.core.experiment.Store method)
shuffle() (in module vivarium.processes.translation)
simulate_compartment_in_experiment() (in module vivarium.core.composition)
simulate_experiment() (in module vivarium.core.composition)
simulate_growth_division() (in module vivarium.processes.multibody_physics)
simulate_motility() (in module vivarium.processes.multibody_physics)
simulate_process() (in module vivarium.core.composition)
simulate_process_in_experiment() (in module vivarium.core.composition)
simulate_transport_metabolism() (in module vivarium.compartments.transport_metabolism)
Sine (class in vivarium.core.experiment)
single_agent_config() (in module vivarium.processes.multibody_physics)
specification() (in module vivarium.experiments.chemotaxis)
split_units() (in module vivarium.data.spreadsheets)
start_polymerizing() (vivarium.library.polymerize.Polymerase method)
state_for() (vivarium.core.experiment.Store method)
state_when() (vivarium.library.polymerize.BindingSite method)
StaticField (class in vivarium.processes.static_field)
StaticLattice (class in vivarium.compartments.static_lattice)
step() (vivarium.library.polymerize.Elongation method)
Store
(class in vivarium.core.experiment)
store_partial() (vivarium.library.polymerize.Elongation method)
Stores
str_to_tuple_keys() (in module vivarium.library.dict_utils)
strength_from() (vivarium.library.polymerize.Template method)
surface_area_from_length() (in module vivarium.processes.derive_globals)
surpassed() (vivarium.states.chromosome.Domain method)
swap_synonyms() (in module vivarium.library.cobra_fba)
symbol() (in module vivarium.library.regulation_logic)
T
Template
(class in vivarium.library.polymerize)
(class in vivarium.processes.template_process)
Template Specification
Template Specifications
template_from_exchange() (vivarium.library.rate_law_utilities.RateLawUtilities method)
template_from_reactions() (vivarium.library.rate_law_utilities.RateLawUtilities method)
template_products() (in module vivarium.library.polymerize)
Templates
term() (in module vivarium.library.regulation_logic)
terminate_replication() (vivarium.states.chromosome.Chromosome method)
terminates_at() (vivarium.library.polymerize.Template method)
Terminator (class in vivarium.library.polymerize)
terminator_distance() (vivarium.states.chromosome.Chromosome method)
test_add_dict() (vivarium.core.experiment.TestUpdateIn method)
test_add_leaf() (vivarium.core.experiment.TestUpdateIn method)
test_add_to_root() (vivarium.core.experiment.TestUpdateIn method)
test_antibiotic_transport() (in module vivarium.processes.antibiotic_transport)
test_antibiotics_composite_similar_to_reference() (in module vivarium.compartments.antibiotics)
test_arpeggio() (in module vivarium.library.regulation_logic)
test_BiGG_metabolism() (in module vivarium.processes.metabolism)
test_canonical() (in module vivarium.library.cobra_fba)
test_chemotaxis_master() (in module vivarium.compartments.chemotaxis_master)
test_chromosome() (in module vivarium.states.chromosome)
test_colony_too_diffuse() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_compartment() (in module vivarium.core.composition)
test_complex_merge() (vivarium.core.experiment.TestUpdateIn method)
test_complexation() (in module vivarium.processes.complexation)
test_concave() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_convenience_kinetics() (in module vivarium.processes.convenience_kinetics)
test_convenience_kinetics_correlated_to_reference() (in module vivarium.processes.convenience_kinetics)
test_convex() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_death_freeze_state() (in module vivarium.processes.death)
test_demo() (in module vivarium.library.cobra_fba)
test_deriver() (in module vivarium.processes.derive_globals)
test_diffusion_field() (in module vivarium.processes.diffusion_field)
test_diffusion_network() (in module vivarium.processes.diffusion_network)
test_expression() (in module vivarium.processes.minimal_expression)
(in module vivarium.processes.ode_expression)
test_expression_chemotaxis() (in module vivarium.compartments.chemotaxis_flagella)
test_fba() (in module vivarium.library.cobra_fba)
test_find_multiple_colonies() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_flagella_expression() (in module vivarium.compartments.flagella_expression)
test_flagella_metabolism() (in module vivarium.compartments.flagella_expression)
test_gene_expression() (in module vivarium.compartments.gene_expression)
test_ignore_outliers_and_nan() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_in() (in module vivarium.core.experiment)
test_injector() (in module vivarium.processes.injector)
test_inverse_topology() (in module vivarium.core.experiment)
test_kinetics() (in module vivarium.library.kinetic_rate_laws)
test_lattice() (in module vivarium.compartments.lattice)
test_make_media() (in module vivarium.library.make_media)
test_master() (in module vivarium.compartments.master)
test_mem_potential() (in module vivarium.processes.membrane_potential)
test_minimal() (in module vivarium.library.cobra_fba)
test_multi() (in module vivarium.core.experiment)
test_multibody() (in module vivarium.library.pymunk_multibody)
(in module vivarium.processes.multibody_physics)
test_no_cells() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_ode_expression_chemotaxis() (in module vivarium.compartments.chemotaxis_flagella)
test_parallel() (in module vivarium.core.experiment)
test_process_deletion() (vivarium.core.composition.TestSimulateProcess method)
test_recursive_store() (in module vivarium.core.experiment)
test_rna_degradation() (in module vivarium.processes.degradation)
test_set_root() (vivarium.core.experiment.TestUpdateIn method)
test_simple() (vivarium.core.experiment.TestUpdateIn method)
test_sine() (in module vivarium.core.experiment)
test_single_cell() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_static_lattice() (in module vivarium.compartments.static_lattice)
test_timescales() (in module vivarium.core.experiment)
test_topology_ports() (in module vivarium.core.experiment)
test_toy_metabolism() (in module vivarium.processes.metabolism)
test_transcription() (in module vivarium.processes.transcription)
test_translation() (in module vivarium.processes.translation)
test_transport() (in module vivarium.processes.Kremling2007_transport)
test_two_cells() (vivarium.processes.derive_colony_shape.TestDeriveColonyShape method)
test_txp_mtb_ge() (in module vivarium.compartments.transport_metabolism)
test_variable_chemotaxis() (in module vivarium.compartments.chemotaxis_flagella)
TestConvienceKinetics (class in vivarium.parameters.parameters)
TestDeriveColonyShape (class in vivarium.processes.derive_colony_shape)
TestSimulateProcess (class in vivarium.core.composition)
TestUpdateIn (class in vivarium.core.experiment)
THRESHOLD (vivarium.core.composition.ToyLinearGrowthDeathProcess attribute)
time_indexed_timeseries_from_data() (in module vivarium.core.emitter)
TimelineProcess (class in vivarium.processes.timeline)
Timepoint
Timepoints
Timeseries
timeseries_from_data() (in module vivarium.core.emitter)
timeseries_to_ndarrays() (in module vivarium.core.composition)
TimeSeriesEmitter (class in vivarium.core.emitter)
timestamp() (in module vivarium.core.experiment)
Timestep
Timesteps
to_dict() (vivarium.library.datum.Datum method)
top() (vivarium.core.experiment.Store method)
Topologies
Topology
topology_ports() (vivarium.core.experiment.Store method)
topology_state() (vivarium.core.experiment.Store method)
toy_transport() (in module vivarium.processes.metabolism)
ToyAntibioticInjector (class in vivarium.processes.death)
ToyCompartment (class in vivarium.core.composition)
ToyDeath (class in vivarium.core.composition)
(class in vivarium.processes.death)
ToyDeriveVolume (class in vivarium.core.composition)
ToyLinearGrowthDeathProcess (class in vivarium.core.composition)
ToyMetabolism (class in vivarium.core.composition)
ToyTransport (class in vivarium.core.composition)
Transcript (class in vivarium.processes.translation)
Transcription (class in vivarium.processes.transcription)
transcripts_to_gene_counts() (in module vivarium.processes.translation)
Translation (class in vivarium.processes.translation)
Transport (class in vivarium.processes.Kremling2007_transport)
TransportLookup (class in vivarium.processes.transport_lookup)
TransportMetabolism (class in vivarium.compartments.transport_metabolism)
traverse() (in module vivarium.states.chromosome)
Tree
TreeMass (class in vivarium.processes.tree_mass)
Trees
tuple_key() (in module vivarium.library.regulation_logic)
tuple_to_str_keys() (in module vivarium.library.dict_utils)
tuplify_port_dicts() (in module vivarium.library.dict_utils)
U
UNBOUND_RIBOSOME_KEY (in module vivarium.processes.translation)
UNBOUND_RNAP_KEY (in module vivarium.processes.transcription)
units (in module vivarium.library.units)
unocclude() (vivarium.library.polymerize.Polymerase method)
Update
update() (vivarium.core.experiment.Experiment method)
(vivarium.core.process.ParallelProcess method)
(vivarium.processes.cellular_potts.CPM method)
update_adhesion_matrix() (vivarium.processes.cellular_potts.CPM method)
update_bodies() (vivarium.library.pymunk_multibody.PymunkMultibody method)
update_body() (vivarium.library.pymunk_multibody.PymunkMultibody method)
update_in() (in module vivarium.core.experiment)
update_screen() (vivarium.library.pymunk_multibody.NullScreen method)
update_subschema() (vivarium.core.experiment.Store method)
update_target_areas() (vivarium.processes.cellular_potts.CPM method)
Updater
Updaters
Updates
V
value_in_embedded_dict() (in module vivarium.library.dict_utils)
Variable
Variables
(class in vivarium.processes.derive_colony_shape)
visit_add() (vivarium.library.make_media.RecipeConstructor method)
visit_break() (vivarium.library.make_media.RecipeConstructor method)
visit_counts() (vivarium.library.make_media.RecipeConstructor method)
visit_inf() (vivarium.library.make_media.RecipeConstructor method)
visit_ingredient() (vivarium.library.make_media.RecipeConstructor method)
visit_media_id() (vivarium.library.make_media.RecipeConstructor method)
visit_numeric() (vivarium.library.make_media.RecipeConstructor method)
visit_one_event() (vivarium.library.make_media.RecipeConstructor method)
visit_one_ingredient() (vivarium.library.make_media.RecipeConstructor method)
visit_recipe() (vivarium.library.make_media.RecipeConstructor method)
visit_timeline() (vivarium.library.make_media.RecipeConstructor method)
visit_volume() (vivarium.library.make_media.RecipeConstructor method)
visit_ws() (vivarium.library.make_media.RecipeConstructor method)
vivarium (module)
vivarium.analysis (module)
vivarium.analysis.analyze (module)
vivarium.compartments (module)
vivarium.compartments.antibiotics (module)
vivarium.compartments.chemotaxis_flagella (module)
vivarium.compartments.chemotaxis_master (module)
vivarium.compartments.chemotaxis_minimal (module)
vivarium.compartments.flagella_expression (module)
vivarium.compartments.gene_expression (module)
vivarium.compartments.gfp_expression (module)
vivarium.compartments.growth_division (module)
vivarium.compartments.growth_division_minimal (module)
vivarium.compartments.injected_glc_phosphorylation (module)
vivarium.compartments.lattice (module)
vivarium.compartments.master (module)
vivarium.compartments.static_lattice (module)
vivarium.compartments.transport_metabolism (module)
vivarium.core (module)
vivarium.core.composition (module)
vivarium.core.emitter (module)
vivarium.core.experiment (module)
vivarium.core.process (module)
vivarium.data (module)
vivarium.data.amino_acids (module)
vivarium.data.chromosomes (module)
vivarium.data.chromosomes.flagella_chromosome (module)
vivarium.data.chromosomes.gfp_chromosome (module)
vivarium.data.chromosomes.toy_chromosome (module)
vivarium.data.flat (module)
vivarium.data.flat.media (module)
vivarium.data.json_files (module)
vivarium.data.knowledge_base (module)
vivarium.data.molecular_weight (module)
vivarium.data.nucleotides (module)
vivarium.data.proteins (module)
vivarium.data.spreadsheets (module)
vivarium.data.synonyms (module)
vivarium.experiments (module)
vivarium.experiments.chemotaxis (module)
vivarium.experiments.glucose_phosphorylation (module)
vivarium.experiments.mother_machine (module)
vivarium.library (module)
vivarium.library.cobra_fba (module)
vivarium.library.datum (module)
vivarium.library.dict_utils (module)
vivarium.library.fasta (module)
vivarium.library.flux_conversion (module)
vivarium.library.kinetic_rate_laws (module)
vivarium.library.look_up (module)
vivarium.library.make_media (module)
vivarium.library.make_network (module)
vivarium.library.path (module)
vivarium.library.polymerize (module)
vivarium.library.pretty (module)
vivarium.library.pymunk_multibody (module)
vivarium.library.rate_law_utilities (module)
vivarium.library.regulation_logic (module)
vivarium.library.timeseries (module)
vivarium.library.units (module)
vivarium.parameters (module)
vivarium.parameters.parameters (module)
vivarium.plots (module)
vivarium.plots.colonies (module)
vivarium.plots.metabolism (module)
vivarium.plots.multibody_physics (module)
vivarium.plots.transport_metabolism (module)
vivarium.processes (module)
vivarium.processes.antibiotic_transport (module)
vivarium.processes.cellular_potts (module)
vivarium.processes.complexation (module)
vivarium.processes.convenience_kinetics (module)
vivarium.processes.death (module)
vivarium.processes.degradation (module)
vivarium.processes.derive_colony_shape (module)
vivarium.processes.derive_concentrations (module)
vivarium.processes.derive_counts (module)
vivarium.processes.derive_globals (module)
vivarium.processes.diffusion_field (module)
vivarium.processes.diffusion_network (module)
vivarium.processes.division_volume (module)
vivarium.processes.glucose_phosphorylation (module)
vivarium.processes.growth (module)
vivarium.processes.growth_protein (module)
vivarium.processes.injector (module)
vivarium.processes.Kremling2007_transport (module)
vivarium.processes.membrane_potential (module)
vivarium.processes.meta_division (module)
vivarium.processes.metabolism (module)
vivarium.processes.minimal_expression (module)
vivarium.processes.multibody_physics (module)
vivarium.processes.nonspatial_environment (module)
vivarium.processes.ode_expression (module)
vivarium.processes.static_field (module)
vivarium.processes.template_process (module)
vivarium.processes.timeline (module)
vivarium.processes.transcription (module)
vivarium.processes.translation (module)
vivarium.processes.transport_lookup (module)
vivarium.processes.tree_mass (module)
vivarium.states (module)
vivarium.states.chromosome (module)
volume_from_length() (in module vivarium.processes.derive_globals)
W
WCM
Whole-Cell Model
Whole-Cell Models
without() (in module vivarium.core.experiment)
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