Stochastic Histogram Output Format Request

[Chris Andersen]

Hello VCell community,

I am working with a non-spatial stochastic simulation from one of the published papers in the VCell compendium and I have had excellent results so far, but there is one nuance to how the results from VCell are output that could be better for my purposes.

I am working to develop a causal computational modeling framework with the goal of predicting the effects of interventions (e.g. genetic ablations, drug treatments, etc) on signaling networks. While I have had incredible success in using VCell to generate various control and intervention settings with the model I have been using, the output from VCell's stochastic histogram mode for a time-point of interest does not tell me run-specific joint observations across all the molecules in the simulation. Instead, I get a breakdown of each of the unique quantities per molecule and their relative frequencies

As a demonstrative example, I have attached a screenshot of the results of a toy example of my stochastic simulation using only three molecules across 4 trials:

Unfortunately, I have no idea which counts co-occur together, I only know how frequently they occurred across all four trials. In my analysis workflow, I end up using these distribution parameters to generate pseudo-empirical joint observations so I can ultimately calculate joint distributions of variables, but this essentially assumes uniform distributions across joint observations, which may or may not actually be the case.

Let me know if this is not enough information, unclear, or infeasible within VCell. I am very interested to know if this can be done! Thank you for your consideration and hope to hear back soon.

Sincerely,

Chris Andersen