Index

_

_handle_parallel_process() (in module vivarium.core.process)

A

ABM access() (vivarium.core.registry.Registry method) add() (vivarium.core.store.Store method) add_composer() (vivarium.core.composer.MetaComposer method) add_composers() (vivarium.core.composer.MetaComposer method) add_node() (vivarium.core.store.Store method) Agent-Based Model Agent-based model agent-based model Agent-Based Models Agent-based models

agent-based models apply_defaults() (vivarium.core.store.Store method) apply_func() (in module vivarium.core.emitter) apply_update() (vivarium.core.engine.Engine method) (vivarium.core.store.Store method) assemble_data() (in module vivarium.core.emitter) assert_no_divide() (in module vivarium.core.registry) assoc_in() (in module vivarium.core.process) assoc_path() (in module vivarium.library.topology) ATTRIBUTE_READ_COMMANDS (vivarium.core.process.Process attribute) ATTRIBUTE_WRITE_COMMANDS (vivarium.core.process.Process attribute)

B

Boundary Store boundary store Boundary Stores

boundary stores breakdown_data() (in module vivarium.core.emitter) build_topology_views() (vivarium.core.store.Store method)

C

calculate_mass() (in module vivarium.processes.tree_mass) calculate_timestep() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) can_deserialize() (vivarium.core.registry.Serializer method) (vivarium.core.serialize.DictDeserializer method) (vivarium.core.serialize.SequenceDeserializer method) (vivarium.core.serialize.UnitsSerializer method) client_dict (vivarium.core.emitter.DatabaseEmitter attribute) compare_pid() (vivarium.core.process.ToyParallelProcess method) Compartment compartment Compartment Hierarchy compartment hierarchy Compartments compartments Composer

composer Composer (class in vivarium.core.composer) Composite composite Composite (class in vivarium.core.composer) CompositeDict (in module vivarium.core.types) Composites composites condition_path() (vivarium.core.process.ParallelProcess property) (vivarium.core.process.Process property) connect() (vivarium.core.store.Store method) Control (class in vivarium.core.control) convert_path() (in module vivarium.core.store) convert_path_style() (in module vivarium.library.topology) create() (vivarium.core.store.Store method) create_indexes() (vivarium.core.emitter.DatabaseEmitter class method)

D

d (vivarium.library.topology.TestUpdateIn attribute) data_from_database() (in module vivarium.core.emitter) data_to_database() (in module vivarium.core.emitter) DatabaseEmitter (class in vivarium.core.emitter) Datum (class in vivarium.library.datum) default_host (vivarium.core.emitter.DatabaseEmitter attribute) default_state() (vivarium.core.composer.Composite method) (vivarium.core.process.Process method) defaults (vivarium.core.composer.Composer attribute) (vivarium.core.composer.Composite attribute) (vivarium.core.process.Process attribute) (vivarium.core.process.ToySerializedProcess attribute) (vivarium.core.process.ToySerializedProcessInheritance attribute) (vivarium.library.datum.Datum attribute) (vivarium.processes.tree_mass.TreeMass attribute) Defer (class in vivarium.core.engine) delete() (vivarium.core.store.Store method) delete_experiment() (in module vivarium.core.emitter) delete_experiment_from_database() (in module vivarium.core.emitter) delete_in() (in module vivarium.library.topology) depth() (vivarium.core.store.Store method) Deriver deriver

Deriver (in module vivarium.core.process) Derivers derivers deserialize() (vivarium.core.registry.Serializer method) (vivarium.core.serialize.DictDeserializer method) (vivarium.core.serialize.SequenceDeserializer method) (vivarium.core.serialize.UnitsSerializer method) deserialize_value() (in module vivarium.core.serialize) dict_to_paths() (in module vivarium.library.topology) DictDeserializer (class in vivarium.core.serialize) divide() (vivarium.core.store.Store method) divide_binomial() (in module vivarium.core.registry) divide_null() (in module vivarium.core.registry) divide_set() (in module vivarium.core.registry) divide_set_value() (in module vivarium.core.registry) divide_split() (in module vivarium.core.registry) divide_split_dict() (in module vivarium.core.registry) divide_value() (vivarium.core.store.Store method) divide_zero() (in module vivarium.core.registry) Divider divider divider_registry (in module vivarium.core.registry) Dividers dividers

E

Embedded Timeseries Embedded timeseries embedded timeseries emit() (vivarium.core.emitter.DatabaseEmitter method) (vivarium.core.emitter.Emitter method) (vivarium.core.emitter.NullEmitter method) (vivarium.core.emitter.RAMEmitter method) emit_data() (vivarium.core.store.Store method) Emitter emitter Emitter (class in vivarium.core.emitter) emitter_registry (in module vivarium.core.registry) Emitters emitters

empty_front() (in module vivarium.core.engine) EmptyDefer (class in vivarium.core.engine) end() (vivarium.core.engine.Engine method) (vivarium.core.process.ParallelProcess method) Engine engine Engine (class in vivarium.core.engine) Exchange exchange Exchanges exchanges Experiment experiment Experiments experiments

F

fields() (vivarium.library.datum.Datum method) find_numpy_and_non_strings() (in module vivarium.core.serialize) Flow flow Flow (in module vivarium.core.types)

flow (vivarium.core.composer.Composite attribute) Flows flows format_dict() (in module vivarium.library.pretty) FunctionSerializer (class in vivarium.core.serialize)

G

generate() (vivarium.core.composer.Composer method) (vivarium.core.process.Process method) (vivarium.core.store.Store method) generate_flow() (vivarium.core.composer.Composer method) (vivarium.core.composer.MetaComposer method) (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) generate_processes() (vivarium.core.composer.Composer method) (vivarium.core.composer.MetaComposer method) (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) generate_state() (in module vivarium.core.store) generate_steps() (vivarium.core.composer.Composer method) (vivarium.core.composer.MetaComposer method) (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) generate_store() (vivarium.core.composer.Composer method) (vivarium.core.composer.Composite method) generate_topology() (vivarium.core.composer.Composer method) (vivarium.core.composer.MetaComposer method) (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) generate_value() (vivarium.core.store.Store method) get() (vivarium.core.engine.Defer method) (vivarium.core.engine.EmptyDefer method) get_atlas_client() (in module vivarium.core.emitter) get_atlas_database_emitter_config() (in module vivarium.core.emitter) get_command_result() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) get_composite_from_store() (in module vivarium.core.composer)

get_config() (vivarium.core.store.Store method) get_data() (vivarium.core.emitter.DatabaseEmitter method) (vivarium.core.emitter.Emitter method) (vivarium.core.emitter.RAMEmitter method) get_data_chunks() (in module vivarium.core.emitter) get_data_deserialized() (vivarium.core.emitter.Emitter method) get_data_unitless() (vivarium.core.emitter.Emitter method) get_emitter() (in module vivarium.core.emitter) get_experiment_database() (in module vivarium.core.emitter) get_flow() (vivarium.core.store.Store method) get_history_data_db() (in module vivarium.core.emitter) get_in() (in module vivarium.library.topology) (vivarium.core.store.Store method) get_local_client() (in module vivarium.core.emitter) get_parameters() (vivarium.core.composer.Composer method) (vivarium.core.composer.Composite method) get_path() (vivarium.core.store.Store method) get_path_timeseries() (vivarium.core.emitter.Emitter method) get_paths() (vivarium.core.store.Store method) get_private_state() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) get_processes() (vivarium.core.store.Store method) get_query() (in module vivarium.core.emitter) get_schema() (vivarium.core.process.Process method) get_steps() (vivarium.core.store.Store method) get_template() (vivarium.core.store.Store method) get_timeseries() (vivarium.core.emitter.Emitter method) get_topology() (vivarium.core.store.Store method) get_value() (vivarium.core.store.Store method) get_values() (vivarium.core.store.Store method) get_variable_title() (in module vivarium.plots.simulation_output)

H

Hierarchies hierarchies Hierarchy

hierarchy hierarchy_depth() (in module vivarium.core.store) HierarchyPath (in module vivarium.core.types)

I

initial_state() (vivarium.core.composer.Composer method) (vivarium.core.composer.Composite method) (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) (vivarium.processes.tree_mass.TreeMass method) Inner inner inner_value() (vivarium.core.store.Store method)

insert() (vivarium.core.store.Store method) insert_topology() (in module vivarium.core.store) inverse_topology() (in module vivarium.library.topology) invert_topology() (in module vivarium.core.engine) is_deriver() (vivarium.core.process.Process method) is_float() (in module vivarium.core.control) is_step() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) (vivarium.core.process.Step method)

K

key_for_value() (in module vivarium.core.store)

L

list() (vivarium.core.registry.Registry method)

M

make_dir() (in module vivarium.core.control) make_fallback_serializer_function() (in module vivarium.core.serialize) Masking masking merge() (vivarium.core.composer.Composite method) merge_overrides() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) MetaComposer (class in vivarium.core.composer) METHOD_COMMANDS (vivarium.core.process.Process attribute) module vivarium.core.composer vivarium.core.control vivarium.core.emitter vivarium.core.engine vivarium.core.process vivarium.core.registry vivarium.core.serialize vivarium.core.store vivarium.core.types vivarium.library.datum vivarium.library.pretty vivarium.library.topology vivarium.plots.simulation_output vivarium.processes.tree_mass

move() (vivarium.core.store.Store method) MSM Multiscale Model Multiscale model multiscale model Multiscale Models Multiscale models multiscale models

N

name (vivarium.processes.tree_mass.TreeMass attribute) next_update() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) (vivarium.core.process.ToyParallelProcess method) (vivarium.core.process.ToySerializedProcess method) (vivarium.core.process.ToySerializedProcessInheritance method) (vivarium.processes.tree_mass.TreeMass method)

normalize_path() (in module vivarium.library.topology) NullEmitter (class in vivarium.core.emitter) NumpyFallbackSerializer (class in vivarium.core.serialize)

O

Outer outer

outer_path() (vivarium.core.store.Store method) OutputDict (in module vivarium.core.types)

P

parallel() (vivarium.core.process.Process property) ParallelProcess (class in vivarium.core.process) parameters() (vivarium.core.process.ParallelProcess property) (vivarium.core.process.Process property) parse_args() (vivarium.core.control.Control method) Path path Path Timeseries Path timeseries path timeseries path_for() (vivarium.core.store.Store method) path_timeseries_from_data() (in module vivarium.core.emitter) path_timeseries_from_embedded_timeseries() (in module vivarium.core.emitter) path_to() (vivarium.core.store.Store method) Paths paths paths_to_dict() (in module vivarium.library.topology) pf() (in module vivarium.core.engine) plot_simulation_output() (in module vivarium.plots.simulation_output) plot_variables() (in module vivarium.plots.simulation_output) Port port Ports ports ports() (vivarium.core.process.Process method) ports_schema() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) (vivarium.core.process.ToyParallelProcess method) (vivarium.core.process.ToySerializedProcess method) (vivarium.core.process.ToySerializedProcessInheritance method) (vivarium.processes.tree_mass.TreeMass method)

pp() (in module vivarium.core.engine) pre_send_command() (vivarium.core.process.Process method) print_progress_bar() (in module vivarium.core.engine) Process process Process (class in vivarium.core.process) Process Class Process class process class Process Classes Process classes process classes Process Command Process command process command Process Commands Process commands process commands process_registry (in module vivarium.core.registry) Processes processes Processes (in module vivarium.core.types) processes (vivarium.core.composer.Composite attribute) ProcessSerializer (class in vivarium.core.serialize) python_type (vivarium.core.registry.Serializer attribute)

Q

QuantitySerializer (class in vivarium.core.serialize)

R

RAMEmitter (class in vivarium.core.emitter) Raw Data Raw data raw data recursive_end_process() (vivarium.core.store.Store method) register() (vivarium.core.registry.Registry method) Registry (class in vivarium.core.registry) RFC RFC 2119, [1], [2]

run_command() (vivarium.core.process.Process method) run_command_method() (vivarium.core.process.Process method) run_experiment() (vivarium.core.control.Control method) run_for() (vivarium.core.engine.Engine method) run_library_cli() (in module vivarium.core.control) run_one_plot() (vivarium.core.control.Control method) run_plots() (vivarium.core.control.Control method) run_steps() (vivarium.core.engine.Engine method) run_workflow() (vivarium.core.control.Control method)

S

saved_data (vivarium.core.emitter.SharedRamEmitter attribute) Schema schema Schema (in module vivarium.core.types) schema (vivarium.library.datum.Datum attribute) Schema Key Schema key schema key Schema Key-Value Pair Schema key-value pair schema key-value pair Schema Key-Value Pairs Schema key-value pairs schema key-value pairs Schema Keys Schema keys schema keys Schema Value Schema value schema value Schema Values Schema values schema values schema() (vivarium.core.process.ParallelProcess property) (vivarium.core.process.Process property) schema_keys (vivarium.core.store.Store attribute) schema_override() (vivarium.core.process.ParallelProcess property) (vivarium.core.process.Process property) schema_topology() (vivarium.core.store.Store method) Schemas schemas send_command() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) (vivarium.core.process.ToyParallelProcess method) SequenceDeserializer (class in vivarium.core.serialize) serialize() (vivarium.core.registry.Serializer method) (vivarium.core.serialize.FunctionSerializer method) (vivarium.core.serialize.NumpyFallbackSerializer method) (vivarium.core.serialize.ProcessSerializer method) (vivarium.core.serialize.QuantitySerializer method) (vivarium.core.serialize.SetSerializer method) (vivarium.core.serialize.UnitsSerializer method)

serialize_value() (in module vivarium.core.serialize) Serializer serializer Serializer (class in vivarium.core.registry) serializer_registry (in module vivarium.core.registry) Serializers serializers set_axes() (in module vivarium.plots.simulation_output) set_emit_value() (vivarium.core.store.Store method) set_emit_values() (vivarium.core.store.Store method) set_path() (vivarium.core.store.Store method) set_value() (vivarium.core.store.Store method) SetSerializer (class in vivarium.core.serialize) SharedRamEmitter (class in vivarium.core.emitter) starts_with() (in module vivarium.core.engine) State (in module vivarium.core.types) state (vivarium.core.composer.Composite attribute) state_for() (vivarium.core.store.Store method) Step step Step (class in vivarium.core.process) Steps steps Steps (in module vivarium.core.types) steps (vivarium.core.composer.Composite attribute) Store store Store (class in vivarium.core.store) Store API store API Stores stores

T

Template template Template Specification Template specification template specification Template Specifications Template specifications template specifications Templates templates TestUpdateIn (class in vivarium.library.topology) Timepoint timepoint Timepoints timepoints Timeseries timeseries timeseries_from_data() (in module vivarium.core.emitter) timestamp() (in module vivarium.core.engine) Timestep timestep

Timesteps timesteps to_dict() (vivarium.library.datum.Datum method) top() (vivarium.core.store.Store method) Topologies topologies Topology topology Topology (in module vivarium.core.types) topology (vivarium.core.composer.Composite attribute) topology_path() (in module vivarium.core.store) topology_state() (vivarium.core.store.Store method) toy_control() (in module vivarium.core.control) toy_plot() (in module vivarium.core.control) ToyParallelProcess (class in vivarium.core.process) ToySerializedProcess (class in vivarium.core.process) ToySerializedProcessInheritance (class in vivarium.core.process) Tree tree TreeMass (class in vivarium.processes.tree_mass) Trees trees

U

UnitsSerializer (class in vivarium.core.serialize) Update update Update (in module vivarium.core.types) update() (vivarium.core.engine.Engine method) update_accumulate() (in module vivarium.core.registry) update_condition() (vivarium.core.process.ParallelProcess method) (vivarium.core.process.Process method) update_dictionary() (in module vivarium.core.registry) update_in() (in module vivarium.library.topology)

update_merge() (in module vivarium.core.registry) update_nonnegative_accumulate() (in module vivarium.core.registry) update_null() (in module vivarium.core.registry) update_set() (in module vivarium.core.registry) Updater updater updater_registry (in module vivarium.core.registry) Updaters updaters Updates updates

V

Variable variable Variables variables view_values() (in module vivarium.core.store) vivarium.core.composer module vivarium.core.control module vivarium.core.emitter module vivarium.core.engine module vivarium.core.process module vivarium.core.registry module

vivarium.core.serialize module vivarium.core.store module vivarium.core.types module vivarium.library.datum module vivarium.library.pretty module vivarium.library.topology module vivarium.plots.simulation_output module vivarium.processes.tree_mass module

W

WCM Whole-Cell Model Whole-cell model whole-cell model

Whole-Cell Models Whole-cell models whole-cell models write_emit() (vivarium.core.emitter.DatabaseEmitter method)