The SimBiology Desktop offers a number of different plot types that can be chosen in a task window. The default plot type in a simulation task, for example, is the Time plot, which plots states against the simulation time:

Three items need to be configured for this plot type:

• tobj …

In the first part I presented a workflow to export a SimBiology model as well as data to the workspace from the SimBiology Desktop, speed up its simulation and prepare it for parallel computation. Here I will set up the actual optimization problem.
The Optimization solvers usually only accept a …

Under some circumstances the parameter estimation tasks built into SimBiology® (sbioparamestim and sbionlinfit) and the SimBiology Desktop (sbionlinfit) are not robust enough for the given data, the model or the initial parameter values.

If the objective function has many local minima - which is nearly always the case for complex systems …