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Package Documentation

  • Introduction
    • What is COMETSpy?
    • How to use this Documentation:
    • Cite Us:
  • Installation
    • Installation of COMETS
  • COMETS Capabilities
    • Capabilities in space
    • Biological capabilities
    • Computational capabilities

Tutorials

  • Getting started
    • Preparing a model for COMETS
    • Setting COMETS simulation parameters
      • Preparing a COMETS simulation layout
      • Running a COMETS simulation
      • Checking simulation output and possible errors
      • Accessing the results of the simulation
  • Growth in a test tube
    • Loading the COMETS Python Toolbox
    • Creating a test tube
    • Loading a model
    • Setting the simulation parameters
    • Running the simulation
    • Analyzing the results
  • Two-species competition assay
    • Load models and create a mutant
    • Create layout, add models and set up media composition
    • Set up simulation parameters
    • Run the simulation
    • Simulating serial transfers
  • Citrate utilization in the Long Term Evolution Experiment.
  • Crossfeeding in a chemostat
  • Simulating evolution
    • Load the model
    • Set up the layout
    • Set up simulation parameters
    • Run the simulation
    • Visualize the results
  • Growth of a circular colony
  • Growth of a branching colony
  • Growth and propagation of bacterial colonies on flat surfaces
  • Simulating growth on Petri dish
  • Soil-air interface

API

  • cometspy package
    • cometspy.comets module
    • cometspy.layout module
    • cometspy.model module
    • cometspy.params module
    • cometspy.utils module
    • Module contents
COMETSpy
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