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Compartmental Modeling Software (CMS) 0.9 beta documentation - Home Compartmental Modeling Software (CMS) 0.9 beta documentation - Home
  • Introduction to compartmental modeling
  • Introduction to the software
  • Input and output reference
  • Glossary
  • IDM docs
  • GitHub
  • Introduction to compartmental modeling
  • Introduction to the software
  • Input and output reference
  • Glossary
  • IDM docs
  • GitHub

Section Navigation

  • Model file syntax
    • Custom propensity function
    • Create a spatial model
  • Configuration file syntax
    • Solvers
      • Exact methods
      • Approximate methods
      • Spatial simulation methods
      • Rare event probability estimation
      • Exploratory methods
    • Output
    • Random number library
  • Input and output reference
  • Configuration file syntax
  • Solvers
  • Exact methods

Exact methods#

Assuming a homogeneously mixed system, these methods are exact in that every reaction firing and its time are computed explicitly. While exact, these methods can be computationally expensive.

  • Gillespie (SSA)
  • GillespieFirstReaction
  • Gibson-Bruck next reaction
  • Hybrid SSA

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Solvers

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Gillespie (SSA)

  • Introduction to compartmental modeling
  • Introduction to the software
  • Input and output reference
  • Glossary

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