API Reference
ecoliecoli.analysisecoli.analysis.antibiotics_colonyecoli.analysis.antibiotics_colony.amp_plotsecoli.analysis.antibiotics_colony.explorationecoli.analysis.antibiotics_colony.load_dataecoli.analysis.antibiotics_colony.metricsecoli.analysis.antibiotics_colony.plotecoli.analysis.antibiotics_colony.plot_utilsecoli.analysis.antibiotics_colony.snapshot_and_hist_plotecoli.analysis.antibiotics_colony.spatial_correlationecoli.analysis.antibiotics_colony.tet_dry_massecoli.analysis.antibiotics_colony.timeseriesecoli.analysis.antibiotics_colony.validation
ecoli.analysis.causality_networkecoli.analysis.colonyecoli.analysis.multidaughterecoli.analysis.multiexperimentecoli.analysis.multigenerationecoli.analysis.multiseedecoli.analysis.multivariantecoli.analysis.single
ecoli.compositesecoli.experimentsecoli.libraryecoli.library.cell_wallecoli.library.create_timelineecoli.library.data_predicatesecoli.library.initial_conditionsecoli.library.json_stateecoli.library.kinetic_rate_lawsecoli.library.lattice_utilsecoli.library.logging_toolsecoli.library.parametersecoli.library.parquet_emitterecoli.library.pymunk_multibodyecoli.library.schemaecoli.library.serializeecoli.library.sim_dataecoli.library.unitsecoli.library.updaters
ecoli.processesecoli.processes.chemotaxisecoli.processes.environmentecoli.processes.environment.derive_globalsecoli.processes.environment.diffusion_fieldecoli.processes.environment.exchangeecoli.processes.environment.exchange_dataecoli.processes.environment.field_timelineecoli.processes.environment.local_fieldecoli.processes.environment.lysisecoli.processes.environment.media_updateecoli.processes.environment.multibody_physicsecoli.processes.environment.reaction_diffusion_field
ecoli.processes.listenersecoli.processes.listeners.RNA_countsecoli.processes.listeners.aggregatorecoli.processes.listeners.dna_supercoilingecoli.processes.listeners.mass_listenerecoli.processes.listeners.monomer_countsecoli.processes.listeners.replication_dataecoli.processes.listeners.ribosome_dataecoli.processes.listeners.rna_synth_probecoli.processes.listeners.rnap_dataecoli.processes.listeners.unique_molecule_counts
ecoli.processes.membraneecoli.processes.spatialityecoli.processes.stubsecoli.processes.allocatorecoli.processes.bulk_timelineecoli.processes.cell_divisionecoli.processes.chemostatecoli.processes.chromosome_replicationecoli.processes.chromosome_structureecoli.processes.complexationecoli.processes.concentrations_deriverecoli.processes.division_detectorecoli.processes.engine_processecoli.processes.enzyme_kineticsecoli.processes.equilibriumecoli.processes.global_clockecoli.processes.metabolismecoli.processes.metabolism_reduxecoli.processes.metabolism_redux_classicecoli.processes.partitionecoli.processes.polypeptide_elongationecoli.processes.polypeptide_initiationecoli.processes.protein_degradationecoli.processes.registriesecoli.processes.rna_degradationecoli.processes.rna_interferenceecoli.processes.rna_maturationecoli.processes.shapeecoli.processes.tf_bindingecoli.processes.tf_unbindingecoli.processes.transcript_elongationecoli.processes.transcript_initiationecoli.processes.two_component_systemecoli.processes.unique_update
ecoli.variants
reconstructionreconstruction.ecolireconstruction.ecoli.compendiumreconstruction.ecoli.dataclassesreconstruction.ecoli.dataclasses.processreconstruction.ecoli.dataclasses.statereconstruction.ecoli.dataclasses.adjustmentsreconstruction.ecoli.dataclasses.common_namesreconstruction.ecoli.dataclasses.constantsreconstruction.ecoli.dataclasses.getter_functionsreconstruction.ecoli.dataclasses.growth_rate_dependent_parametersreconstruction.ecoli.dataclasses.molecule_groupsreconstruction.ecoli.dataclasses.molecule_idsreconstruction.ecoli.dataclasses.relation
reconstruction.ecoli.scriptsreconstruction.ecoli.fit_sim_data_1reconstruction.ecoli.knowledge_base_rawreconstruction.ecoli.simulation_data
reconstruction.testsreconstruction.spreadsheets
runscriptsvalidationwholecellwholecell.iowholecell.testswholecell.tests.iowholecell.tests.utilswholecell.tests.utils.profile_polymerizewholecell.tests.utils.test_blaswholecell.tests.utils.test_datawholecell.tests.utils.test_dependency_graphwholecell.tests.utils.test_fast_nnlswholecell.tests.utils.test_filepathwholecell.tests.utils.test_library_performancewholecell.tests.utils.test_mc_complexationwholecell.tests.utils.test_memory_debugwholecell.tests.utils.test_modular_fbawholecell.tests.utils.test_nf_glpkwholecell.tests.utils.test_polymerizewholecell.tests.utils.test_unit_struct_arraywholecell.tests.utils.test_units
wholecell.utilswholecell.utils.build_odewholecell.utils.constantswholecell.utils.datawholecell.utils.dependency_graphwholecell.utils.fast_nonnegative_least_squareswholecell.utils.filepathwholecell.utils.fittingwholecell.utils.forkedPdbwholecell.utils.make_mediawholecell.utils.mc_complexationwholecell.utils.memory_debugwholecell.utils.modular_fbawholecell.utils.parallelizationwholecell.utils.plotting_toolswholecell.utils.polymerizewholecell.utils.profilerwholecell.utils.protein_countswholecell.utils.randomwholecell.utils.sparklinewholecell.utils.spatial_toolwholecell.utils.test_parallelizationwholecell.utils.toyawholecell.utils.unit_struct_arraywholecell.utils.unitswholecell.utils.voronoi_plot_main