Step 5: Calculating a Time Course


In the tree on the left under Tasks you can find the entry called Time Course. Selecting this entry in the tree will bring you to the time course settings dialog.

(Click here to go to the Time Course dialog)

Here you can set all parameters for calculating a time course like starting time, end time, how many data points are to be stored and last but not least the method for calculating the trajectory. So far you can choose between deterministic simulation or stochastic simulation. Depending on the simulation method, you have some more parameters that can be changed in the table toward the bottom of the dialog, but the default values should suffice most of the time.

figure: Time Course dialog

Before we can calculate the actual trajectory, we have to specify a report definition to use for the output and a filename for this report definition. To do this, you have to click on the "ReportDefinition" button at the bottom. In the dialog that pops up, you choose the report definition that you created in the last step and specify a file name in the Target field. You can either type the filename, or browse the file system by clicking the "browse" button. When you are finished, click the "confirm" button. You are now ready to calculate the time course by clicking the "Run" button at the bottom of the Time Course dialog. To verify that copasi really did calculate something, look at the file you just specified, it should now contain the data of the time course simulation.