vivarium package

Subpackages

• vivarium.actor package
  • Submodules
    • vivarium.actor.actor module
    • vivarium.actor.boot module
    • vivarium.actor.control module
    • vivarium.actor.event module
    • vivarium.actor.filepath module
    • vivarium.actor.inner module
    • vivarium.actor.outer module
    • vivarium.actor.shepherd module
    • vivarium.actor.stub module
  • Module contents
• vivarium.analysis package
  • Submodules
    • vivarium.analysis.analyze module
  • Module contents
• vivarium.compartments package
  • Submodules
    • vivarium.compartments.antibiotics module
    • vivarium.compartments.chemotaxis_flagella module
    • vivarium.compartments.chemotaxis_master module
    • vivarium.compartments.chemotaxis_minimal module
    • vivarium.compartments.flagella_expression module
    • vivarium.compartments.gene_expression module
    • vivarium.compartments.gfp_expression module
    • vivarium.compartments.growth_division module
    • vivarium.compartments.growth_division_minimal module
    • vivarium.compartments.injected_glc_phosphorylation module
      • Toy Injected Glucose Phosphorylation Compartment
    • vivarium.compartments.lattice module
    • vivarium.compartments.master module
    • vivarium.compartments.static_lattice module
    • vivarium.compartments.transport_metabolism module
  • Module contents
• vivarium.core package
  • Submodules
    • vivarium.core.composition module
    • vivarium.core.emitter module
    • vivarium.core.experiment module
      • Experiment and Store Classes
    • vivarium.core.process module
      • Process and Compartment Classes
  • Module contents
• vivarium.data package
  • Subpackages
    • vivarium.data.chromosomes package
      • Submodules
        • vivarium.data.chromosomes.flagella_chromosome module
        • vivarium.data.chromosomes.gfp_chromosome module
        • vivarium.data.chromosomes.toy_chromosome module
      • Module contents
    • vivarium.data.flat package
      • Subpackages
        • vivarium.data.flat.media package
          • Module contents
      • Module contents
    • vivarium.data.json_files package
      • Module contents
  • Submodules
    • vivarium.data.amino_acids module
    • vivarium.data.knowledge_base module
    • vivarium.data.molecular_weight module
    • vivarium.data.nucleotides module
    • vivarium.data.proteins module
    • vivarium.data.spreadsheets module
    • vivarium.data.synonyms module
  • Module contents
• vivarium.experiments package
  • Submodules
    • vivarium.experiments.chemotaxis module
      • Chemotaxis Experiments
    • vivarium.experiments.colony_metrics_experiment module
    • vivarium.experiments.glucose_phosphorylation module
      • Toy Glucose Phosphorylation Experiment
    • vivarium.experiments.lattice_experiment module
    • vivarium.experiments.mother_machine module
  • Module contents
• vivarium.library package
  • Submodules
    • vivarium.library.cobra_fba module
    • vivarium.library.datum module
    • vivarium.library.dict_utils module
    • vivarium.library.fasta module
    • vivarium.library.flux_conversion module
    • vivarium.library.kinetic_rate_laws module
    • vivarium.library.look_up module
    • vivarium.library.make_media module
    • vivarium.library.make_network module
    • vivarium.library.path module
    • vivarium.library.polymerize module
    • vivarium.library.pretty module
    • vivarium.library.pymunk_multibody module
    • vivarium.library.rate_law_utilities module
    • vivarium.library.regulation_logic module
    • vivarium.library.timeseries module
    • vivarium.library.units module
      • Units
  • Module contents
• vivarium.parameters package
  • Submodules
    • vivarium.parameters.parameters module
  • Module contents
• vivarium.plots package
  • Submodules
    • vivarium.plots.Mears2014_flagella_activity module
    • vivarium.plots.Vladimirov2008_motor module
    • vivarium.plots.colonies module
      • Colony Plotting Tools
    • vivarium.plots.metabolism module
    • vivarium.plots.multibody_physics module
    • vivarium.plots.transport_metabolism module
  • Module contents
• vivarium.processes package
  • Submodules
    • vivarium.processes.Endres2006_chemoreceptor module
    • vivarium.processes.Kremling2007_transport module
    • vivarium.processes.Mears2014_flagella_activity module
    • vivarium.processes.Vladimirov2008_motor module
    • vivarium.processes.antibiotic_transport module
      • Simulate Antibiotic Import and Export
    • vivarium.processes.cellular_potts module
    • vivarium.processes.complexation module
    • vivarium.processes.convenience_kinetics module
      • Convenience Kinetics
        • Bibliography
    • vivarium.processes.death module
      • Model of Conditional Cell Death
        • Death Detector Classes
        • Death Process Classes
    • vivarium.processes.degradation module
    • vivarium.processes.derive_colony_shape module
      • Colony Shape Deriver
    • vivarium.processes.derive_concentrations module
    • vivarium.processes.derive_counts module
    • vivarium.processes.derive_globals module
    • vivarium.processes.diffusion_field module
      • Diffusion Field
    • vivarium.processes.diffusion_network module
    • vivarium.processes.division_volume module
    • vivarium.processes.glucose_phosphorylation module
      • Toy Glucose Phosphorylation Process
    • vivarium.processes.growth module
    • vivarium.processes.growth_protein module
    • vivarium.processes.injector module
      • Injector Process
    • vivarium.processes.membrane_potential module
    • vivarium.processes.meta_division module
    • vivarium.processes.metabolism module
      • Metabolism Process
    • vivarium.processes.minimal_expression module
    • vivarium.processes.multibody_physics module
      • Multibody physics process
    • vivarium.processes.nonspatial_environment module
    • vivarium.processes.ode_expression module
      • Ordinary Differential Equation Expression Model
    • vivarium.processes.static_field module
    • vivarium.processes.template_process module
    • vivarium.processes.timeline module
    • vivarium.processes.toxin-antitoxin module
    • vivarium.processes.transcription module
      • Stochastic Transcription
    • vivarium.processes.translation module
      • Stochastic Translation
    • vivarium.processes.transport_lookup module
    • vivarium.processes.tree_mass module
  • Module contents
• vivarium.states package
  • Submodules
    • vivarium.states.chromosome module
  • Module contents

Module contents