A tool for fitting to data the output of a complex simulation involving possibly many runs with different stimulus protocols each with several recordings.
When saved in a session, e.g. fit.ses, two companion files are created called fit.ses.ft1 and fit.ses.fd1. The *.ft1 file contains a readable (and modifiable) definition of the protocols and parameters. The *.fd1 file contains a copy of the data and internal parameters of the panels. When the fit.ses is retrieved, these two files are also read to rebuild the state of the MulRunFitter.
Because it generally takes a long time and a lot of effort to enter the information necessary to specify a complete multiple run fit strategy, it is a good idea to often save the partially built fitter in a session so that if something goes wrong you can always exit and start up again at a safe point.
The usage of the MulRunFitter is expected to undergo considerable refinement in the future.
Pressing the ErrorValue button will execute the "Generator" protocols and show the total error between simulation and data at this particular point in parameter space.
The Parameters menu is used primarily to add, remove, and change parameter names or expressions. Parameter names can be any variable name or any statement involving $1. Statements involving $1 are extremely useful in causing a single parameter to modify many variables. e.g. forall Ra = $1 or some_procedure($1) Even if the parameter is a single variable name, it is most often more useful to express it as a "normalized expression" so that all "optimized" values are close to unity. e.g. cai0_ca_ion = 1e-4*$1 The Praxis fitter does not work efficiently (or at all) when parameters have very different scales. (but see the log scale factor discussion below)
It also creates panels for:
When the Append the path to savepath.fit checkbox is checked, the elapsed time, fitting error value, and parameters are appended to a file called savepath.fit every time the error value is reduced by a call to the error function..
The Running checkbox is on when the optimizer is running. You should not do much gui interaction at this time such as opening new windows or pressing buttons that could potentially interfere with the protocol runs. First press the Stop button (may need to press it several times) to stop the optimizer. The Optimize button starts the fitting process.
The Generators menu is used to add and view stimulus protocols (which include error functions for calculating the difference between simulation results and data). Each generator is a generalization of a Run Fitter.
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