Step 4: Creating a Report Definition


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.

(Click here to go to the Report definition dialog.)

figure: empty Report Definition Dialog

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.

figure: Object Browser dialog

Likewise click the check box for the time attribute which you will find directly under the node for the model (same level as the Metabolites node). Once you have selected all the attributes for the output, you finish the selection by clicking the "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.

figure: Report Definition dialog with entries