Before you can execute a parameter estimation task you need to specify the dataset which COPASI will use to fit the parameters you have specified. Each experiment of your dataset contributes to the objective function with the following weighted sum of squares:

Where is the currently tested parameter set, is a point in the dataset, and the corresponding simulated value. The indices and denote columns and rows in the dataset. The weight for each data column is given by . COPASI provides 3 methods shown in the table below to calculate the weights for you. After applying the method chosen COPASI scales the weights so that for each experiment the maximal occurring weight is 1. In case that the weights calculated are not satisfactory you are able to manually override them individually.

Table 4.1. Weight Calculation Methods

Name	Formula
Mean
Mean Square
Standard Deviation

To specify the experimental data you click on the Experimental Data button at the top right of the parameter estimation dialog. A new dialog opens that lets you enter experimental data.

Experimental Data Dialog

To read a data file, click on the open button beside the label File at the top of the dialog and choose a file that contains experimental data from the file dialog. The data file should contain experimental data grouped in experiments. To support automatic detection of experiments these must be separated by one or more empty lines. But manually definition of experiments is allowed. The data for an experiment must be a table of values. The columns of the table are separated by a user specifiable separation character. The default and recommended character is the <tab>-character. The first line of each experiment is treated as the row containing the column headings. However, this is only a default and the header row can be specified by the user. The header row may be anywhere in the file the data is contained. The purpose of the header row is to ease the interface to the data file and may be omitted. To tell COPASI that no header row is included uncheck the box next to the header. Once COPASI has read a file, you have to specify some information for each experiment included in the file. To select an experiment you choose it from the right selection box. The first thing you need to specify is whether the data belongs to a Steady-State analysis or to a time course simulation. You also have to associate the individual rows of input data to elements of the model. For this, you click on the ... button in each row and select the corresponding object in the selection dialog. It is mandatory that COPASI knows about the meaning of each data column. The data in a column can have four different types, which are:

If you don't want COPASI to use the whole dataset of an experiment, but only a subset, you can specify the start and end line for this subset. You also may delete experiments completely. If you do so, you may notice that the New Document will be enabled. Pressing it will add the first not used experiment of the currently active file. Since it is commonly the case that all experimental data within one file has the same format, COPASI allows you to copy information of experimental data from the previous to the current or form the current to the next experiment within a file by selecting from previous and to next. If COPASI detects that experimental data descriptions are identical it will automatically set the from previous check box and disable editing the current experiment. Should you want to modify it you will have to unmark the check box first.

If you have more than one file, you can load additional data files and process them in the same manner. Once you are finished defining your datasets for the fitting, you close the data dialog with the OK button. Before you can start the parameter estimation process, you have to choose the method by which the fitting will be done and maybe set some method parameters. Most of the time, the default parameter values should do. The method choosing is done at the bottom of the dialog by selecting the method from the drop down list. For an explanation of the individual methods, please consult the methods section.

If you want to have output from the parameter estimation task, you have to create an output definition as described in the Output section or you choose the default report named "Parameter Fitting". The default reports prints a description of the settings you provided for this parameter fitting run, intermediate results every time the target function improves, and a detailed result at the end. The easiest way to get a customized output is probably to use the output assistant which you activate via the Output Assistant button. This is described in the Output Assistant section. All that is left to do in order to write the output to a specific file is to connect an output definition with a file. This can be achieved by clicking on the Report button. This opens a dialog that lets you connect the report for a specific task to a file on your hard disk. First we choose a report that is suitable for the parameter estimation task from the drop down list at the top of the dialog. Next, we specify a file that will be used to store the report by clicking on the browse button and selecting the destination in the file dialog that opens. Per default, COPASI creates a new file or overwrites an existing file with the same name. Alternatively, you can tell COPASI to append the report to the end of an existing file by selecting the corresponding check box labeled Append at the bottom of the dialog. Once you are finished, you click on the Confirm button. If you now run the task, COPASI will write the output to the file you specified.

Parameter Estimation Results

After running a Parameter Estimation task the result may be viewed by selecting the Result widget. This result widget contains multiple tabs. The overall fit and performance statistic are displayed in the Main and detailed information about parameters, experiments, and fitted values can be found under the corresponding tabs. In addition, you may look at the correlation matrix of the parameters or the Fisher information matrix.