Now that we have a model, we could actually go ahead and do a simulation. But
in order for copasi to know what to do with the calculated data from the
simulation, we have to define some which kind of output we want. This can
either be a plot (which we will do a later) or a report. If we
don’t define an output , copasi will not store the results.
In order to create a report definition, you navigate in the tree to
Output->Reports
and click the "new"
button on the bottom and then on the "commit"
button. If you now double click on the new entry in the table you will find
yourself in the dialog for the report definition.
At first the list widget is empty, that means that nothing will be put into the
report. In order to add items for the output, you click on the "+"
button which
is located to the right of the empty list. This will open the Object Browser
dialog where you can select any available object. For now, we will limit
ourselves to the time object and the concentrations of the metabolites.
If you look at the tree, you will see one node that has the name of your model
as specified in Step 1. Opening this node will show you all the objects
available in the model. Now open the Metabolites node and in the metabolites
subtree you open the Attribute list node and in there you will find the
Concentration node. Open the Concentration node and click the check boxes with the names of the metabolites.
"OK"
button.
The attributes that you see in the list widget now, will be written to file
in same the order as the appear in the list. If you want the time
to appear in the first column of your output instead of the last, you have to change the order of the selected elements.
You can change the order of the elements by selecting an item in the list and moving it up or down via the arrow buttons on the left.
You can also delete an element by selecting it and then pushing the "-"
button.