After you have defined all reactions that make up your model, you can proceed to perform calculations in COPASI. For some tasks, the results are displayed in a separate dialog, and saving them to a file may not be necessary. However, for other tasks—such as a time course simulation—it is often useful or required to save the results (like the trajectory) to a file or create a plot for visual inspection.
To store results or generate plots in COPASI, you need to define a report and associate it with a file, or define a plot. (Later in this section, we also describe an alternative, though less flexible, way to save time course simulation results.)
COPASI provides a list of predefined reports suitable for some calculation tasks. These are described in the next section. If you prefer to create your own plots or reports, you can use the Output Assistant (the easy way), or define the output manually (for greater flexibility), as described in this chapter.
