It was noticed that in VCell models that were exported to SBML-OMEX, spatial results seemed to be weird. Compared to their VCML counterparts, the results did not seem to match up, nor did the results seem reasonable.
It has been determined that the root cause was that unit transformations in VCell did not apply to the extent and origin of the geometry. This resulted in the associated equations being wrong by magnitudes, and affecting the results entirely.
For a robust fix, not only do the global extent and origin need to be scaled, but any analytical geometry must also be scaled accordingly.
CodeByDrescher
commented
6 months ago
It was noticed that in VCell models that were exported to SBML-OMEX, spatial results seemed to be weird. Compared to their VCML counterparts, the results did not seem to match up, nor did the results seem reasonable.
It has been determined that the root cause was that unit transformations in VCell did not apply to the extent and origin of the geometry. This resulted in the associated equations being wrong by magnitudes, and affecting the results entirely.
For a robust fix, not only do the global extent and origin need to be scaled, but any analytical geometry must also be scaled accordingly.