Input and output reference

This section describes all input and output options available in CMS. For example, the syntax used in the model file used to define the mathematics of the model, the random number libraries and solvers available to use in the configuration file, and the different output reports that can be created.

• Model file syntax
  • Basic EMODL syntax
  • Mathematical operators and functions
    • Unary
    • Binary
    • N-ary
  • Example
    • Custom propensity function
    • Create a spatial model
• Configuration file syntax
  • Example
    • Solvers
      • Exact methods
        • Gillespie (SSA)
          • Example
        • GillespieFirstReaction
          • Example
        • Gibson-Bruck next reaction
          • Example
        • Hybrid SSA
          • Example
      • Approximate methods
        • BLeaping
          • Example
        • RLeaping
          • Example
        • Tau-leaping
          • Example
      • Spatial simulation methods
        • Diffusive finite state projection (DFSP)
          • Example
        • FractionalDiffusion (FD)
          • Example
        • TransportSSA (ISSA)
          • Example
      • Rare event probability estimation
        • Doubly weighted stochastic simulation algorithm (dwSSA)
          • Example
        • State-dependent doubly weighted stochastic simulation algorithm (sdwSSA)
          • Example
      • Exploratory methods
        • ExitTimes
          • Example
        • Midpoint tau-leaping
          • Example
        • RLeapingFast
          • Example
        • OptimalTransportSSA (OTSSA)
          • Example
    • Output
      • Example
    • Random number library
      • Example