All modules for which code is available
- builtins
- 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.buildCausalityNetwork
- ecoli.analysis.causality_network.build_network
- ecoli.analysis.causality_network.network_components
- ecoli.analysis.causality_network.read_dynamics
- ecoli.analysis.colony.snapshots
- ecoli.analysis.multigeneration.new_gene_counts
- ecoli.analysis.multiseed.ecocyc_table
- ecoli.analysis.multiseed.subgenerational_expression_table
- ecoli.analysis.multivariant.average_monomer_counts
- ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps
- ecoli.analysis.single.blame
- ecoli.analysis.single.mass_fraction_summary
- ecoli.composites.chemotaxis_minimal
- ecoli.composites.ecoli_master
- ecoli.composites.ecoli_master_tests
- ecoli.composites.ecoli_spatial
- ecoli.composites.environment.grow_divide
- ecoli.composites.environment.lattice
- 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.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.parquet_emitter
- ecoli.library.pymunk_multibody
- ecoli.library.schema
- ecoli.library.serialize
- ecoli.library.sim_data
- ecoli.library.units
- ecoli.library.updaters
- ecoli.processes.allocator
- ecoli.processes.bulk_timeline
- ecoli.processes.cell_division
- ecoli.processes.chemostat
- ecoli.processes.chemotaxis.chemoreceptor_cluster
- ecoli.processes.chemotaxis.coarse_motor
- ecoli.processes.chemotaxis.flagella_motor
- 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.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.enzyme_kinetics
- ecoli.processes.equilibrium
- ecoli.processes.global_clock
- 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.membrane_potential
- 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.rna_degradation
- ecoli.processes.rna_interference
- ecoli.processes.rna_maturation
- ecoli.processes.shape
- ecoli.processes.spatiality.diffusion_network
- ecoli.processes.spatiality.spatial_geometry
- ecoli.processes.stubs.exchange_stub
- ecoli.processes.stubs.exchanger_stub
- 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.condition
- ecoli.variants.new_gene_internal_shift
- ecoli.variants.variant_test
- numba
- numpy.random.mtrand
- reconstruction.ecoli.compendium.growth_data
- reconstruction.ecoli.dataclasses.adjustments
- reconstruction.ecoli.dataclasses.common_names
- reconstruction.ecoli.dataclasses.constants
- reconstruction.ecoli.dataclasses.getter_functions
- reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters
- reconstruction.ecoli.dataclasses.molecule_groups
- reconstruction.ecoli.dataclasses.molecule_ids
- reconstruction.ecoli.dataclasses.process.chromosome_structure
- reconstruction.ecoli.dataclasses.process.complexation
- reconstruction.ecoli.dataclasses.process.equilibrium
- reconstruction.ecoli.dataclasses.process.metabolism
- reconstruction.ecoli.dataclasses.process.process
- reconstruction.ecoli.dataclasses.process.replication
- reconstruction.ecoli.dataclasses.process.rna_decay
- reconstruction.ecoli.dataclasses.process.transcription
- reconstruction.ecoli.dataclasses.process.transcription_regulation
- reconstruction.ecoli.dataclasses.process.translation
- reconstruction.ecoli.dataclasses.process.two_component_system
- reconstruction.ecoli.dataclasses.relation
- reconstruction.ecoli.dataclasses.state.bulkMolecules
- reconstruction.ecoli.dataclasses.state.external_state
- reconstruction.ecoli.dataclasses.state.internal_state
- reconstruction.ecoli.dataclasses.state.stateFunctions
- reconstruction.ecoli.dataclasses.state.uniqueMolecules
- reconstruction.ecoli.fit_sim_data_1
- reconstruction.ecoli.knowledge_base_raw
- reconstruction.ecoli.scripts.fold_changes.calculate_fc
- reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat
- reconstruction.ecoli.scripts.metabolite_concentrations.merge_files
- reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat
- reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat
- reconstruction.ecoli.scripts.update_biocyc_files
- reconstruction.ecoli.simulation_data
- reconstruction.spreadsheets
- reconstruction.tests.test_fit_sim_data_1
- reconstruction.tests.test_spreadsheets
- runscripts.analysis
- runscripts.create_variants
- runscripts.debug.compare_pickles
- runscripts.parca
- runscripts.workflow
- validation.ecoli.scripts.rnaDegRates
- validation.ecoli.validation_data
- validation.ecoli.validation_data_raw
- wholecell.io.tsv
- wholecell.tests.io.test_tsv
- wholecell.tests.utils.test_blas
- wholecell.tests.utils.test_data
- wholecell.tests.utils.test_dependency_graph
- wholecell.tests.utils.test_fast_nnls
- wholecell.tests.utils.test_filepath
- wholecell.tests.utils.test_library_performance
- wholecell.tests.utils.test_mc_complexation
- wholecell.tests.utils.test_memory_debug
- wholecell.tests.utils.test_modular_fba
- wholecell.tests.utils.test_nf_glpk
- wholecell.tests.utils.test_polymerize
- wholecell.tests.utils.test_unit_struct_array
- wholecell.tests.utils.test_units
- wholecell.utils._build_sequences
- wholecell.utils._fastsums
- wholecell.utils.build_ode
- wholecell.utils.data
- wholecell.utils.dependency_graph
- wholecell.utils.fast_nonnegative_least_squares
- wholecell.utils.filepath
- wholecell.utils.fitting
- wholecell.utils.forkedPdb
- wholecell.utils.make_media
- wholecell.utils.mc_complexation
- wholecell.utils.memory_debug
- wholecell.utils.parallelization
- wholecell.utils.plotting_tools
- wholecell.utils.polymerize
- wholecell.utils.profiler
- wholecell.utils.protein_counts
- wholecell.utils.random
- wholecell.utils.sparkline
- wholecell.utils.spatial_tool
- wholecell.utils.test_parallelization
- wholecell.utils.toya
- wholecell.utils.unit_struct_array
- wholecell.utils.units
- wholecell.utils.voronoi_plot_main