Analyze the accuracy of a linear approximations for model kinetics

Objectives

• Assess how well an SBML is approximated by one or more linear models based on
  • Consistency of Jacobian
  • Accuracy of reproducing a non-linear simulation
• Identify "linearity bottleneck" reactions, those that must limit the viability of a linear approximation

Tuning SystemDiscovery

• Need sufficient data, maybe in the 1000s.
• Reduce threshold (sensitivity) to get more sparse coefficients
• Set includebias = True
• Don't include boundary species

Analyses

Versions