LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
configs/__init__.py
ecoli/__init__.py
ecoli/analysis/__init__.py
ecoli/analysis/antibiotics_colony/__init__.py
ecoli/analysis/antibiotics_colony/amp_plots.py
ecoli/analysis/antibiotics_colony/exploration.py
ecoli/analysis/antibiotics_colony/load_data.py
ecoli/analysis/antibiotics_colony/metrics.py
ecoli/analysis/antibiotics_colony/plot.py
ecoli/analysis/antibiotics_colony/plot_utils.py
ecoli/analysis/antibiotics_colony/snapshot_and_hist_plot.py
ecoli/analysis/antibiotics_colony/spatial_correlation.py
ecoli/analysis/antibiotics_colony/tet_dry_mass.py
ecoli/analysis/antibiotics_colony/timeseries.py
ecoli/analysis/antibiotics_colony/validation.py
ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py
ecoli/analysis/antibiotics_colony/subgen_gene_plots/make_fig_1b.py
ecoli/analysis/causality_network/__init__.py
ecoli/analysis/causality_network/buildCausalityNetwork.py
ecoli/analysis/causality_network/build_network.py
ecoli/analysis/causality_network/network_components.py
ecoli/analysis/causality_network/read_dynamics.py
ecoli/analysis/colony/__init__.py
ecoli/analysis/colony/snapshots.py
ecoli/analysis/multidaughter/__init__.py
ecoli/analysis/multiexperiment/__init__.py
ecoli/analysis/multigeneration/__init__.py
ecoli/analysis/multigeneration/new_gene_counts.py
ecoli/analysis/multigeneration/replication.py
ecoli/analysis/multigeneration/ribosome_components.py
ecoli/analysis/multigeneration/ribosome_crowding.py
ecoli/analysis/multigeneration/ribosome_production.py
ecoli/analysis/multigeneration/ribosome_usage.py
ecoli/analysis/multigeneration/rna_decay_03_high.py
ecoli/analysis/multiseed/__init__.py
ecoli/analysis/multiseed/ecocyc_table.py
ecoli/analysis/multiseed/protein_counts_validation.py
ecoli/analysis/multiseed/ribosome_spacing.py
ecoli/analysis/multiseed/subgenerational_expression_table.py
ecoli/analysis/multivariant/__init__.py
ecoli/analysis/multivariant/average_monomer_counts.py
ecoli/analysis/multivariant/cell_mass.py
ecoli/analysis/multivariant/doubling_time_hist.py
ecoli/analysis/multivariant/doubling_time_line.py
ecoli/analysis/multivariant/dummy.py
ecoli/analysis/multivariant/new_gene_translation_efficiency_heatmaps.py
ecoli/analysis/single/__init__.py
ecoli/analysis/single/blame.py
ecoli/analysis/single/mass_fraction_summary.py
ecoli/composites/__init__.py
ecoli/composites/chemotaxis_minimal.py
ecoli/composites/ecoli_master.py
ecoli/composites/ecoli_master_tests.py
ecoli/composites/ecoli_spatial.py
ecoli/composites/environment/__init__.py
ecoli/composites/environment/grow_divide.py
ecoli/composites/environment/lattice.py
ecoli/experiments/__init__.py
ecoli/experiments/antibiotics_tests.py
ecoli/experiments/ecoli_engine_process.py
ecoli/experiments/ecoli_master_sim.py
ecoli/experiments/ecoli_master_sim_tests.py
ecoli/experiments/glt_division.py
ecoli/experiments/metabolism_exchanger.py
ecoli/experiments/metabolism_redux_sim.py
ecoli/experiments/tet_amp_sim.py
ecoli/library/__init__.py
ecoli/library/create_timeline.py
ecoli/library/data_predicates.py
ecoli/library/initial_conditions.py
ecoli/library/json_state.py
ecoli/library/kinetic_rate_laws.py
ecoli/library/lattice_utils.py
ecoli/library/logging_tools.py
ecoli/library/parameters.py
ecoli/library/parquet_emitter.py
ecoli/library/pymunk_multibody.py
ecoli/library/schema.py
ecoli/library/serialize.py
ecoli/library/sim_data.py
ecoli/library/test_parquet_emitter.py
ecoli/library/units.py
ecoli/library/updaters.py
ecoli/library/cell_wall/__init__.py
ecoli/library/cell_wall/column_sampler.py
ecoli/library/cell_wall/fit_lysis_time.py
ecoli/library/cell_wall/hole_detection.py
ecoli/library/cell_wall/lattice.py
ecoli/processes/__init__.py
ecoli/processes/allocator.py
ecoli/processes/bulk_timeline.py
ecoli/processes/cell_division.py
ecoli/processes/chemostat.py
ecoli/processes/chromosome_replication.py
ecoli/processes/chromosome_structure.py
ecoli/processes/complexation.py
ecoli/processes/concentrations_deriver.py
ecoli/processes/division_detector.py
ecoli/processes/engine_process.py
ecoli/processes/enzyme_kinetics.py
ecoli/processes/equilibrium.py
ecoli/processes/global_clock.py
ecoli/processes/metabolism.py
ecoli/processes/metabolism_redux.py
ecoli/processes/metabolism_redux_classic.py
ecoli/processes/partition.py
ecoli/processes/polypeptide_elongation.py
ecoli/processes/polypeptide_initiation.py
ecoli/processes/protein_degradation.py
ecoli/processes/registries.py
ecoli/processes/rna_degradation.py
ecoli/processes/rna_interference.py
ecoli/processes/rna_maturation.py
ecoli/processes/shape.py
ecoli/processes/tf_binding.py
ecoli/processes/tf_unbinding.py
ecoli/processes/transcript_elongation.py
ecoli/processes/transcript_initiation.py
ecoli/processes/two_component_system.py
ecoli/processes/unique_update.py
ecoli/processes/antibiotics/antibiotic_transport_odeint.py
ecoli/processes/antibiotics/antibiotic_transport_steady_state.py
ecoli/processes/antibiotics/cell_wall.py
ecoli/processes/antibiotics/conc_to_counts.py
ecoli/processes/antibiotics/death.py
ecoli/processes/antibiotics/lysis_initiation.py
ecoli/processes/antibiotics/murein_division.py
ecoli/processes/antibiotics/pbp_binding.py
ecoli/processes/antibiotics/permeability.py
ecoli/processes/antibiotics/test_cell_wall.py
ecoli/processes/antibiotics/test_cell_wall_division.py
ecoli/processes/antibiotics/test_lysis_initiation.py
ecoli/processes/antibiotics/tetracycline_ribosome_equilibrium.py
ecoli/processes/chemotaxis/__init__.py
ecoli/processes/chemotaxis/chemoreceptor_cluster.py
ecoli/processes/chemotaxis/coarse_motor.py
ecoli/processes/chemotaxis/flagella_motor.py
ecoli/processes/environment/__init__.py
ecoli/processes/environment/derive_globals.py
ecoli/processes/environment/diffusion_field.py
ecoli/processes/environment/exchange.py
ecoli/processes/environment/exchange_data.py
ecoli/processes/environment/field_timeline.py
ecoli/processes/environment/local_field.py
ecoli/processes/environment/lysis.py
ecoli/processes/environment/media_update.py
ecoli/processes/environment/multibody_physics.py
ecoli/processes/environment/reaction_diffusion_field.py
ecoli/processes/listeners/RNA_counts.py
ecoli/processes/listeners/__init__.py
ecoli/processes/listeners/aggregator.py
ecoli/processes/listeners/dna_supercoiling.py
ecoli/processes/listeners/mass_listener.py
ecoli/processes/listeners/monomer_counts.py
ecoli/processes/listeners/replication_data.py
ecoli/processes/listeners/ribosome_data.py
ecoli/processes/listeners/rna_synth_prob.py
ecoli/processes/listeners/rnap_data.py
ecoli/processes/listeners/unique_molecule_counts.py
ecoli/processes/membrane/__init__.py
ecoli/processes/membrane/membrane_potential.py
ecoli/processes/spatiality/__init__.py
ecoli/processes/spatiality/diffusion_network.py
ecoli/processes/spatiality/spatial_geometry.py
ecoli/processes/stubs/__init__.py
ecoli/processes/stubs/exchange_stub.py
ecoli/processes/stubs/exchanger_stub.py
ecoli/variants/__init__.py
ecoli/variants/condition.py
ecoli/variants/new_gene_internal_shift.py
ecoli/variants/variant_test.py
reconstruction/__init__.py
reconstruction/spreadsheets.py
reconstruction/ecoli/__init__.py
reconstruction/ecoli/fit_sim_data_1.py
reconstruction/ecoli/knowledge_base_raw.py
reconstruction/ecoli/simulation_data.py
reconstruction/ecoli/compendium/__init__.py
reconstruction/ecoli/compendium/growth_data.py
reconstruction/ecoli/dataclasses/__init__.py
reconstruction/ecoli/dataclasses/adjustments.py
reconstruction/ecoli/dataclasses/common_names.py
reconstruction/ecoli/dataclasses/constants.py
reconstruction/ecoli/dataclasses/getter_functions.py
reconstruction/ecoli/dataclasses/growth_rate_dependent_parameters.py
reconstruction/ecoli/dataclasses/molecule_groups.py
reconstruction/ecoli/dataclasses/molecule_ids.py
reconstruction/ecoli/dataclasses/relation.py
reconstruction/ecoli/dataclasses/process/__init__.py
reconstruction/ecoli/dataclasses/process/chromosome_structure.py
reconstruction/ecoli/dataclasses/process/complexation.py
reconstruction/ecoli/dataclasses/process/equilibrium.py
reconstruction/ecoli/dataclasses/process/metabolism.py
reconstruction/ecoli/dataclasses/process/process.py
reconstruction/ecoli/dataclasses/process/replication.py
reconstruction/ecoli/dataclasses/process/rna_decay.py
reconstruction/ecoli/dataclasses/process/transcription.py
reconstruction/ecoli/dataclasses/process/transcription_regulation.py
reconstruction/ecoli/dataclasses/process/translation.py
reconstruction/ecoli/dataclasses/process/two_component_system.py
reconstruction/ecoli/dataclasses/state/__init__.py
reconstruction/ecoli/dataclasses/state/bulkMolecules.py
reconstruction/ecoli/dataclasses/state/external_state.py
reconstruction/ecoli/dataclasses/state/internal_state.py
reconstruction/ecoli/dataclasses/state/stateFunctions.py
reconstruction/ecoli/dataclasses/state/uniqueMolecules.py
reconstruction/ecoli/scripts/__init__.py
reconstruction/ecoli/scripts/update_biocyc_files.py
reconstruction/ecoli/scripts/fold_changes/__init__.py
reconstruction/ecoli/scripts/fold_changes/calculate_fc.py
reconstruction/ecoli/scripts/metabolism_kinetics/__init__.py
reconstruction/ecoli/scripts/metabolism_kinetics/convert_to_flat.py
reconstruction/ecoli/scripts/metabolite_concentrations/__init__.py
reconstruction/ecoli/scripts/metabolite_concentrations/convert_to_flat.py
reconstruction/ecoli/scripts/metabolite_concentrations/merge_files.py
reconstruction/ecoli/scripts/nca/fold_changes.py
reconstruction/ecoli/scripts/nca/nca.py
reconstruction/ecoli/scripts/nca/run_all.py
reconstruction/ecoli/scripts/nca/test_nca.py
reconstruction/ecoli/scripts/protein_half_lives/__init__.py
reconstruction/ecoli/scripts/protein_half_lives/convert_to_flat.py
reconstruction/ecoli/scripts/rna_half_lives/__init__.py
reconstruction/ecoli/scripts/rna_half_lives/convert_to_flat.py
reconstruction/tests/__init__.py
reconstruction/tests/test_fit_sim_data_1.py
reconstruction/tests/test_spreadsheets.py
runscripts/__init__.py
runscripts/analysis.py
runscripts/create_variants.py
runscripts/parca.py
runscripts/sim.py
runscripts/workflow.py
runscripts/debug/__init__.py
runscripts/debug/compare_pickles.py
runscripts/debug/diff_simouts.py
runscripts/debug/process_vulnerabilities.py
validation/__init__.py
validation/ecoli/__init__.py
validation/ecoli/validation_data.py
validation/ecoli/validation_data_raw.py
validation/ecoli/scripts/__init__.py
validation/ecoli/scripts/rnaDegRates.py
vecoli.egg-info/PKG-INFO
vecoli.egg-info/SOURCES.txt
vecoli.egg-info/dependency_links.txt
vecoli.egg-info/requires.txt
vecoli.egg-info/top_level.txt
wholecell/__init__.py
wholecell/io/__init__.py
wholecell/io/tsv.py
wholecell/tests/__init__.py
wholecell/tests/io/__init__.py
wholecell/tests/io/test_tsv.py
wholecell/tests/utils/__init__.py
wholecell/tests/utils/profile_polymerize.py
wholecell/tests/utils/test_blas.py
wholecell/tests/utils/test_data.py
wholecell/tests/utils/test_dependency_graph.py
wholecell/tests/utils/test_fast_nnls.py
wholecell/tests/utils/test_filepath.py
wholecell/tests/utils/test_library_performance.py
wholecell/tests/utils/test_mc_complexation.py
wholecell/tests/utils/test_memory_debug.py
wholecell/tests/utils/test_modular_fba.py
wholecell/tests/utils/test_nf_glpk.py
wholecell/tests/utils/test_polymerize.py
wholecell/tests/utils/test_unit_struct_array.py
wholecell/tests/utils/test_units.py
wholecell/tests/utils/test_workflow_fsspec.py
wholecell/utils/__init__.py
wholecell/utils/_build_sequences.c
wholecell/utils/_build_sequences.pyx
wholecell/utils/_fastsums.c
wholecell/utils/_fastsums.pyx
wholecell/utils/build_ode.py
wholecell/utils/constants.py
wholecell/utils/data.py
wholecell/utils/dependency_graph.py
wholecell/utils/fast_nonnegative_least_squares.py
wholecell/utils/filepath.py
wholecell/utils/fitting.py
wholecell/utils/forkedPdb.py
wholecell/utils/make_media.py
wholecell/utils/mc_complexation.c
wholecell/utils/mc_complexation.pyx
wholecell/utils/memory_debug.py
wholecell/utils/modular_fba.py
wholecell/utils/parallelization.py
wholecell/utils/plotting_tools.py
wholecell/utils/polymerize.py
wholecell/utils/profiler.py
wholecell/utils/protein_counts.py
wholecell/utils/random.py
wholecell/utils/sparkline.py
wholecell/utils/spatial_tool.py
wholecell/utils/test_parallelization.py
wholecell/utils/toya.py
wholecell/utils/unit_struct_array.py
wholecell/utils/units.py
wholecell/utils/voronoi_plot_main.py
wholecell/utils/_netflow/__init__.py
wholecell/utils/_netflow/_base.py
wholecell/utils/_netflow/nf_cplex.py
wholecell/utils/_netflow/nf_glpk.py