Analysis Methods > Optimization > Optimization document

BioUML allows performing diagram parameters estimation by creation of a special optimization document. This document is stored as xml-file and combines all the settings required for the optimization including a list of parameters to fit indicating the search boundaries, parameters of a selected optimization method, solver settings and the experimental data list. When optimization is complete, the resulting parameter values and results of model simulations can be stored as tables and then plotted. To create a new document select tab "Data" at the top pane of the dialog and open folder "Optimization". Then click the left mouse button on "documents" folder and choose item "New optimization" in the pop-up menu. Type the name of the document in the resulting input dialog, select the database and the diagram which you want to operate and press "OK". The existing document can be opened by the double-click. If you want to remove a document, click the left mouse button on it and select item "Remove".

Another way to create an optimization document is as follows. Select tab "Analysis" to the left of tab "Data". Find the optimization methods list in the tree under "Methods" -> "Optimization". Click the left mouse button on the method by which you want to perform optimization and select "Start optimization" in the pop-up menu.

The working area of the optimization document includes the three main windows. The first window located in the lower right corner of the framework is designed to select the optimization options. It includes tabs with optimization method and diagram parameters, experimental data and solver settings. "Method" tab of this window, in particular, contains the buttons to start and stop optimization, to save the results and to draw the plots for their visual presentation. It also informs you about the calculation progress and the best (smallest) values found for the objective and penalty functions up to this time. To the left of this window you can see a short description of the chosen optimization method and links to the base papers for this method programming. Finally the upper right window is intended to store parameters for fitting.