Encode additional features of XPP ODE files into SED-ML

[jonrkarr]

• Global integration options
  • maxstor: total number of time steps that will be kept in memory
  • bound: maximum any plotted variable can reach in magnitude
  • delay: maximum delay allowed in the integration
  • tor_per: period for a toroidal phasespace
  • fold: name of variable to be considered modulo the period
  • autoeval: whether or not to automatically re-evaluate tables everytime a parameter is changed
• range: parameter scans
• stoch: ensemble of stochastic simulations
• 2D axes limits: xlo, xhi, ylo, yhi
• Line type: lt (<1 means plot markers rather than lines)
• 3D plots: axes, xmin, xmax, ymin, ymax, zmin, zmax, phi, theta
• AUTO bifurcation analysis
• Other types of plots
  • Manifold colors: smc, umc
  • Null clines: xnc, ync, nmesh
  • Poincare maps: poimap, poivar, poipln, poisgn, poistop
  • Animations

Executing some of the above through SED-ML requires figuring out how to execute it from the xppaut command line (e.g., AUTO).