What is the simulations file for? #604
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Hi all, I don't understand what the simulations file is for? Best Matthias |
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Replies: 2 comments 3 replies
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It's an optional file in the same format as the measurement file. It is used by the visualisation api. So when you want to plot measured vs simulated, with the visualisation files is when you'd use it. |
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I understand that part, but I don't understand why we need the file and how this should work. The simulations file was generated before the actual optimization, so the values stored in there are not the simulations for the optimal parameters (?). On the other hand it is super simple to plot the actual simulation results with the optimal parameters. If the tool can perform parameter optimization it must be able to simulate all the experiments and the results can just be generated on the fly. Or would the simulation file be generated by the tool at the end of the optimization and added to the PETab problem? |
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Yes, that.
I'd support that. This is currently more of a library thing. |
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the use case is that you want to record what happened when someone ran the parameter estimation, such for example in the benchmark collection my use case is that when I run the petab problem in my tool, I produce a simulation data frame, that I can give to the plotting package. And yes that's not entirely but apparently it was useful enough for someone to have those files around. |
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Perfect. That is how I would use it, i.e., generating the file after the parameter optimization so that the visualization does not have to run the integration. |
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the use case is that you want to record what happened when someone ran the parameter estimation, such for example in the benchmark collection
my use case is that when I run the petab problem in my tool, I produce a simulation data frame, that I can give to the plotting package. And yes that's not entirely but apparently it was useful enough for someone to have those files around.