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” is fine for COPASI but not for Python building in character encoding)

Parameter Estimation

Currently we cannot setup: * Affected experiments section

But these can be done after configuration with ParameterEstimation by opening the GUI, manually configuring the rest of the task and then saving and returning to python.

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