I have implemented a simple model
in SimBiology in 2 versions – both using reversible reactions
- version1: using pre-defined reaction type ‘MassAction’
- version2: using reaction type ‘uknown’
with concentrations A,B [micromole/L], compartments X,Y [L], reaction rates kf,kr [1/h].
See below screenshots of these models:
model version 1
model version 2
One gets two different models but no warnings or bugs for version 2 are flagged.
Version1 is correct, but after pre-processing - the user defined flux is corrected automatically by according volumes.
In Version2 the reaction rate is simply divided by the first volume X – this model is wrong as the volume is applied to the species from the other compartment.
I wonder why the software treats those models differently. The parser shiould have spotted such misformulation with ease (ziped file attached).
Any comments would be very appreciated, Maciej