MANIFEST.in
README.md
requirements.txt
setup.py
vivarium_cell/__init__.py
vivarium_cell.egg-info/PKG-INFO
vivarium_cell.egg-info/SOURCES.txt
vivarium_cell.egg-info/dependency_links.txt
vivarium_cell.egg-info/entry_points.txt
vivarium_cell.egg-info/requires.txt
vivarium_cell.egg-info/top_level.txt
vivarium_cell/analysis/__init__.py
vivarium_cell/analysis/analyze.py
vivarium_cell/bigg_models/__init__.py
vivarium_cell/bigg_models/e_coli_core.json
vivarium_cell/bigg_models/iAF1260b.json
vivarium_cell/composites/__init__.py
vivarium_cell/composites/gene_expression.py
vivarium_cell/composites/growth_division.py
vivarium_cell/composites/growth_division_minimal.py
vivarium_cell/composites/inclusion_body_growth.py
vivarium_cell/composites/injected_glc_phosphorylation.py
vivarium_cell/composites/lattice.py
vivarium_cell/composites/master.py
vivarium_cell/composites/static_lattice.py
vivarium_cell/data/__init__.py
vivarium_cell/data/amino_acids.py
vivarium_cell/data/knowledge_base.py
vivarium_cell/data/molecular_weight.py
vivarium_cell/data/nucleotides.py
vivarium_cell/data/proteins.py
vivarium_cell/data/spreadsheets.py
vivarium_cell/data/synonyms.py
vivarium_cell/data/chromosomes/__init__.py
vivarium_cell/data/chromosomes/flagella_chromosome.py
vivarium_cell/data/chromosomes/gfp_chromosome.py
vivarium_cell/data/chromosomes/toy_chromosome.py
vivarium_cell/data/flat/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.chromosome.Chromosome.fa
vivarium_cell/data/flat/__init__.py
vivarium_cell/data/flat/covert2002_GLC_G6P_flux_bounds.tsv
vivarium_cell/data/flat/covert2002_ecoli_metabolism_met_mw.tsv
vivarium_cell/data/flat/covert2002_exchange_fluxes.tsv
vivarium_cell/data/flat/covert2002_maintenance_biomass_fluxes.tsv
vivarium_cell/data/flat/covert2002_reactions.tsv
vivarium_cell/data/flat/covert2002_regulatory_proteins.tsv
vivarium_cell/data/flat/covert2002_transport.tsv
vivarium_cell/data/flat/lookup_conc_minimal.tsv
vivarium_cell/data/flat/lookup_conc_minimal_minus_oxygen.tsv
vivarium_cell/data/flat/lookup_conc_minimal_plus_amino_acids.tsv
vivarium_cell/data/flat/lookup_flux_minimal.tsv
vivarium_cell/data/flat/lookup_flux_minimal_minus_oxygen.tsv
vivarium_cell/data/flat/lookup_flux_minimal_plus_amino_acids.tsv
vivarium_cell/data/flat/media_recipes.tsv
vivarium_cell/data/flat/timelines_def.tsv
vivarium_cell/data/flat/wcEcoli_biomass.tsv
vivarium_cell/data/flat/wcEcoli_complexationReactions.tsv
vivarium_cell/data/flat/wcEcoli_environment_molecules.tsv
vivarium_cell/data/flat/wcEcoli_genes.tsv
vivarium_cell/data/flat/wcEcoli_proteins.tsv
vivarium_cell/data/flat/wcEcoli_reactions.tsv
vivarium_cell/data/flat/wcEcoli_transport_reactions.tsv
vivarium_cell/data/flat/media/5X_supplement_EZ.tsv
vivarium_cell/data/flat/media/GLC_G6P.tsv
vivarium_cell/data/flat/media/GLC_LCT.tsv
vivarium_cell/data/flat/media/M9.tsv
vivarium_cell/data/flat/media/M9_GLC.tsv
vivarium_cell/data/flat/media/PURE_Fuji_2014.tsv
vivarium_cell/data/flat/media/PURE_Ueda_2010.tsv
vivarium_cell/data/flat/media/__init__.py
vivarium_cell/data/flat/media/ecoli_core_GLC.tsv
vivarium_cell/data/flat/media/wcEcoli_base.tsv
vivarium_cell/data/json_files/__init__.py
vivarium_cell/data/json_files/kinetic_rate_laws_example.json
vivarium_cell/experiments/__init__.py
vivarium_cell/experiments/colony_metrics_experiment.py
vivarium_cell/experiments/glucose_phosphorylation.py
vivarium_cell/experiments/inclusion_experiment.py
vivarium_cell/experiments/lattice_experiment.py
vivarium_cell/experiments/mother_machine.py
vivarium_cell/library/__init__.py
vivarium_cell/library/cobra_fba.py
vivarium_cell/library/fasta.py
vivarium_cell/library/flux_conversion.py
vivarium_cell/library/kinetic_rate_laws.py
vivarium_cell/library/lattice_utils.py
vivarium_cell/library/look_up.py
vivarium_cell/library/make_media.py
vivarium_cell/library/polymerize.py
vivarium_cell/library/pymunk_multibody.py
vivarium_cell/library/rate_law_utilities.py
vivarium_cell/library/regulation_logic.py
vivarium_cell/parameters/parameters.py
vivarium_cell/plots/__init__.py
vivarium_cell/plots/colonies.py
vivarium_cell/plots/expression_survival_dotplot.py
vivarium_cell/plots/gene_expression.py
vivarium_cell/plots/metabolism.py
vivarium_cell/plots/multibody_physics.py
vivarium_cell/processes/__init__.py
vivarium_cell/processes/antibiotic_transport.py
vivarium_cell/processes/complexation.py
vivarium_cell/processes/convenience_kinetics.py
vivarium_cell/processes/death.py
vivarium_cell/processes/degradation.py
vivarium_cell/processes/derive_colony_shape.py
vivarium_cell/processes/derive_globals.py
vivarium_cell/processes/diffusion_cell_environment.py
vivarium_cell/processes/diffusion_cell_environment_ficks.py
vivarium_cell/processes/diffusion_field.py
vivarium_cell/processes/diffusion_network.py
vivarium_cell/processes/division_volume.py
vivarium_cell/processes/glucose_phosphorylation.py
vivarium_cell/processes/growth_protein.py
vivarium_cell/processes/growth_rate.py
vivarium_cell/processes/inclusion_body.py
vivarium_cell/processes/injector.py
vivarium_cell/processes/local_field.py
vivarium_cell/processes/metabolism.py
vivarium_cell/processes/minimal_expression.py
vivarium_cell/processes/multibody_physics.py
vivarium_cell/processes/nonspatial_environment.py
vivarium_cell/processes/ode_expression.py
vivarium_cell/processes/spatial_geometry.py
vivarium_cell/processes/static_field.py
vivarium_cell/processes/transcription.py
vivarium_cell/processes/translation.py
vivarium_cell/reference_data/antibiotic_transport.csv
vivarium_cell/reference_data/antibiotics_compartment.csv
vivarium_cell/reference_data/colony_metrics.csv
vivarium_cell/reference_data/convenience_kinetics.csv
vivarium_cell/reference_data/metabolism.csv
vivarium_cell/reference_data/total_metrics.csv
vivarium_cell/states/__init__.py
vivarium_cell/states/chromosome.py