If you go to the optimization dialog, you will get a screen similar to the one below.
At the top of the dialog you can find an edit line called "e;Method"e;, where optimization method may be selected. Below this edit line you can see a tabbed pane with method parameters and experimental data setting, parameters of diagram simulation and a pane with method description.
Parameters of each method divided into common and specific. The common are the names for database and diagram which you would like to operate during the optimization. Remember that parameter fitting can be done only for the pathway simulations! The specific method parameters are documented in the methods chapter.
To start the parameter estimation perform the following steps.
| 1. | Select the tab called "e;Method parameters"e; and set a database and its diagram names for operating. |
| 2. | Find the parameters and variables of the selected diagram in a diagram parameter editor and set the initial values of these parameters. |
| 3. | Select the parameters for fitting and press the bottom with up arrow. Selected parameters will be added to the end of the table with fitting parameters above. |
| 4. | To delete a parameter from fitting set, select this parameter and press the bottom with down arrow. |
| 5. | Set upper and lower bounds for each parameter to be fitted. |
| 6. | Set the specific method parameters (for detail information about these parameters see the method chapter). |
| 7. | Select the tab called "e;Experimental data"e; and set experimental data for optimization analysis (for details see the experimental data chapter). |
| 8. | Select the tab called "e;Simulation parameters"e; and set parameters for simulation notably select the solver for diagram simulation and set the absolute and the relative tolerance. |
| 9. | Press the bottom "e;Ok"e;. |