Recording individual fluxes on a species that includes multiple mechanisms
Posted: Tue May 02, 2023 3:04 pm
Hello,
I was wondering if there was a way to record the contribution of individual mechanisms that all act on the same species.
For example, intracellular calcium in the cytosol (which would be defined as an rxd.Species()) has multiple mechanisms that affect its concentration. The mechanisms can be defined in rxd as some combination of rxd.Rate()s, rxd.Reaction()s, and rxd.MultiComparmentReaction()s.
Is there a way to parse out and record the effective flux due to each individual mechanism over time? In other words, is it possible to record the calcium flux due to mechanism 1, mechanism 2, ...etc.?
This would be very helpful for debugging purposes and monitoring which mechanism has the largest contribution to the dynamics of a species.
One way that I've tried to do this is to make a "dummy" species, one for each mechanism, and define its rate to be identical to its corresponding mechanism... and then record the dummy species which would provide the calcium concentration output of that mechanism (ie, the integral of calcium flux). However, I think this has only been successful for mechanisms defined as an rxd.Rate(). But for ones defined as a reaction or multi-compartment reaction, they don't seem to work as nicely.
Thank you for any help you can provide!
I was wondering if there was a way to record the contribution of individual mechanisms that all act on the same species.
For example, intracellular calcium in the cytosol (which would be defined as an rxd.Species()) has multiple mechanisms that affect its concentration. The mechanisms can be defined in rxd as some combination of rxd.Rate()s, rxd.Reaction()s, and rxd.MultiComparmentReaction()s.
Is there a way to parse out and record the effective flux due to each individual mechanism over time? In other words, is it possible to record the calcium flux due to mechanism 1, mechanism 2, ...etc.?
This would be very helpful for debugging purposes and monitoring which mechanism has the largest contribution to the dynamics of a species.
One way that I've tried to do this is to make a "dummy" species, one for each mechanism, and define its rate to be identical to its corresponding mechanism... and then record the dummy species which would provide the calcium concentration output of that mechanism (ie, the integral of calcium flux). However, I think this has only been successful for mechanisms defined as an rxd.Rate(). But for ones defined as a reaction or multi-compartment reaction, they don't seem to work as nicely.
Thank you for any help you can provide!