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All QuB's algorithms operate on the Data Source. The Data Source, at upper-right, can be:
To include files in the file list, go to an algorithm's properties (right-click the button) and put checkmarks next to each file. Many algorithms work on only one file; they interpret "file list" as "file."
When the Data Overlap window has an active list, Data Source:list refers to the portion of the checked traces within the lower (hi-res) pane.
Most algorithms write a log of their progress in the Report window (View -> Report). Many publish results in the Results window (View -> Results). Results are stored alongside the data file in the Session File.
When an algorithm is running, there is a progress bar in the upper-right corner. To stop all algorithms, click "Stop tasks". To stop only one task, choose "Tasks" from the "View" menu, select a task and click Stop.
The algorithms which idealize data or solve for rate constants have a common structure. They compute the likelihood (probability) of the data given a model, and search for the model parameters which maximize likelihood. The gradient is the vector of the partial derivative of likelihood with respect to each parameter. The gradient is used to find more likely parameters. A gradient of zeros indicates a (local) maximum. If an algorithm stops with a large gradient, the model may be wrong.
QuB actually works with the log likelihood (LL). QuB's LL is often much larger than log(0<probability<1) because some of the terms are computed from probability distributions; however, this does not affect the maximal parameters.
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