Caveats

This is a list of known problems currently in Pycotools

Non-Ascii Characters

  • Are not supported
  • Do not use unusual characters or naming systems (i.e. A reaction name called “A -> B” will break pycotools)

Parameter Estimation

Currently we cannot setup:

  • Affected experiments in parameter estimations

Units

Not all quantity units are supported. Supported units are:

  • fmol, pmol, nmol, mmol, mol, dimensionless and # (latter for particle numbers)

Assignments

Assignments are not currently supported but will be in a future release. Again, here simply use the COPASI user interface instead.

Duplicate Names

In COPASI we can have (say) a global quantity and a metaboltie with the same name because they are different entities. This is not supported in Pycotools and you must use unique names for every model component

Known Bugs

  • viz.PlotTimeCourseEnsembles doesn’t work properly if user is fitting multiple experiments with multiple conditions (i.e. defined by independent variables)