Difference between revisions of "Apply events (analysis)"

Revision as of 16:32, 12 March 2019

Analysis title

Apply events

Provider

Institute of Systems Biology

Class

ApplyEvents

Plugin

biouml.plugins.modelreduction (Model reduction plug-in)

Parameters:

• Diagram path – Path to the diagram for analysis.
• Table path – Path to the table for analysis.
• Result path – Path to the diagram for analysis.
• Simulation parameters – Simulation parameters.
  • Engine type – Engine type.
  • Engine options – Engine options.
    • Initial time – Initial time.
    • Completion time – Completion time.
    • Time increment – Time increment.
    • Simulator name – Simulator name.
    • Simulator options – Simulator options.
      • Absolute tolerance – Absolute tolerance.
      • Relative tolerance – Relative tolerance.
      • Statistics mode – Statistics mode.
      • Integration method – Integration method (ADAMS or BDF)
      • Inner linear solver type – Inner linear solver type
      • Jacobian approximation type – Jacobian approximation type
      • Steps limit – Limitation for solver steps count
      • Minimum time step – Minimum time step.
      • Maximum time step inverted – 1 / maximum time step.
      • Mu – Upper bandwidth of Banded Jacobian
      • Ml – Lower bandwidth of Banded Jacobian
      • Detect incorrect numbers (NaNs and Infs – If true then simulation will end when NaN or Infinity encountered
    • Code generation type – Type of code generation: if auto then BioUML will try to choose by itself.
    • Constraints violation – How to handle constraints violation in the model.
    • Fast reactions handling – Method to handle fast reactions: either as separate ODE system with very fast rate or as algebraic system.
    • Algebraic solver name – Name of algebraic solver which will be used
    • Algebraic Solver parameters – Parameters of algebraic solver which will be used
      • Maximum iterations – Maximum iterations
      • Function tolerance – Function tolerance
      • Minimal gradient tolerance – Minimal gradient tolerance
      • Points tolerance – Points tolerance