Record when reactions happen

[Dante Kienigiel]

Hello!

1st time COPASI user here. I'm modeling virus replication right now and my particular problem requires that I not only be able to track the concentration of species over time (which I have working), but also when each of the reactions happened. 

Basically, right now my four reactions are replication (RNA -> 2*RNA), degradation (RNA->), assembly (RNA->Virion) and release (Virion->RNA in a different compartment), so if RNA goes up it's ambiguous if it was due to replication or getting virion from another cell, and if it goes down it's ambiguous if it was due to RNA degradation or assembly into virion. Note that I have each of the species & reactions set up with a subindex per compartment, so I have 2 species and 4 reactions per cell (compartment), but 2*N species & ~4*N reactions total (N = number of cells, I put ~4 because not all cells have release reactions but some have more than one to send RNA to different cells).

I could do it the "dirty way" by checking which other species in other cells changed at the exact same time, but that would only work with direct Gillespie (where you don't have multiple reactions in the same timestep) and would require extra computations which I would like to avoid. I could also imagine other scenarios where you couldn't even do it the dirty way (say, if you had two reactions with different rates but the same reactants & products).

I tried using reports (from the COPASI GUI) but it seems like I can only report changes in flux. I also looked at events but also didn't find a way for reactions to trigger it directly from the reactions. If you have other suggestions to set up spread between compartments in a cleaner way that would also be great but right now it's working so it's not that pressing.

Best,

Dante