This section describes how to create or edit a report definition. Keep in mind that you still have to select this
report for the specific calculation task you want to perform. You can do this (and also choose a filename to write
to) using the Report button as described below in the sections about the different tasks.
|Report Table with default Reports
The dialog for defining report definitions is located under the Output->Reports branch in the object tree. Double
clicking on an empty row in the table creates a new report object and opens the dialog for modifying the report
definition. In this dialog, you can specify a name for the report in the Name field. From the Task drop down list,
you can choose for which kind of task this report should be written. So if you want to store the result of a time
course, you should choose Time-Course
here. The report usually stores the results of its task as a table; the
standard separator character for elements in this table is the tab character (\t). If you want to have another
character as the separator field, you have to uncheck the <tab> check box and specify the separator character
or string you want in the Separator field.
Beside the <tab> check box there is another input field labeled Precision. With this field you can specify how
many significant digits are used for numerical output. The default value is 6.
If you want to, you can also add a comment for the report, e.g. you could state what this report is supposed to
Next you have to define the objects that you want to appear in the report. There are two modes to define a report
definition. Per default, the report is laid out as a table. For example, the report for a time course simulation
will write one line per time step and each line will typically contain the time followed by one or more species
concentrations. In the advanced mode activated by clicking on the button labeled Advanced, the report is split up
into three sections, a header, a body and a footer. You can define the output for each of the sections separately by
clicking on the corresponding tab. In order to get back to the standard table layout, you have to click on the
Advanced again. COPASI will warn you that you might loose some information by converting from the advanced report
definition format to the table format.
Let us discuss how to define a report definition with table layout first since you will probably use this most of
the time. To add a new object to the report definition, you have to click on the button labeled Item. This will open
the object browser dialog.
|Simple Object Selection Dialog
The selection dialog shows a tree that contains what we think are the objects that would be most commonly used in
generating report, plots, sliders etc. You select objects by clicking on the corresponding leave in the selection
dialogs tree view. For plots and report, the simple selection dialog will allow you to select several objects at
once. To select a continuous range of objects, you select the first object of the range, then you press and hold the
SHIFT button and select the last object in the range. You can also make non-continuous selection by holding down the
CTRL key while clicking on the object to select/deselect. Also selecting a whole branch in the selection dialog will
select all the leaves under that branch.
If this simple selection dialog does not contain the object that you want to include in your report, you can
activate an extended selection tree by activating the expert mode check box. The tree you now see contains all
objects COPASI knows about. In this tree, the objects belonging to your model are located in the branch that
corresponds to the name of your model. The position of that branch varies since the branches are sorted
alphabetically. The selection that you have already made in the simple selection tree should be preserved, and vice
versa. Any selection you make in the full tree is preserved when you switch back to the simple tree. Each branch of
the full tree has a check box up front which can assume three states. The unchecked state means that no objects in
this subtree are selected. A check mark on a black background means that the whole subtree is selected, i.e. all
objects in this subtree are selected. A check mark on a gray background means that part of the subtree is
|Object Browser Dialog Expert Mode
Due to the model structure, most objects appear more than once in the tree.
So do not be surprised if you select some objects you may be see that not only the selected objects will suddenly
change their selection state. E.g. if you select the whole Compartments subtree of your model, all the species which
are part of the compartments get selected as well, which means that on selecting the Compartments branch, the whole
Species branch changes its state to be selected.
Let us assume you want to define the report for a trajectory task in expert mode. In this case, you will probably
want the time and some or all of the transient concentrations of the species in your report. The time for the time
course is the last item in the Model branch, you select it by clicking on the check box in front of the name. If you
want to add the concentrations of all species, you open the Species sub-branch in the Model branch and open the
Select by attribute branch. There you can select the Concentration attribute. Selecting the Concentration attribute
will select the concentrations for all species. If you only want to have some of the species in your report, you
open the sub-branches of the wanted species in the Species branch and select the Concentration attribute only for
those species. If your model contains many species and you want to have all except one species in your report, it is
often easier to first select all concentrations via the Select by attribute branch and then deselect the one you
don't want, rather then selecting the individual concentrations you want. Once you are finished with selecting the
objects for your report, you confirm the selection by clicking the OK button in the selection dialog. The objects
you selected will now appear in the list box of the report definition dialog.
|Report Definition Dialog
They will appear in the report in the same order as they appear in this list. To reorder the entries in the list,
you can select individual entries and move them up and down in the list with the corresponding buttons on the left
of the list. For example it might be a good idea to move the time object to the top of the list so that it will
appear as the first table column in the file since this is the way most programs would expect it. Also in order to
delete unnecessary items, you just select them and click on the Delete button. The only thing that is now left is to
connect this report to a file. This has to be done in the dialog for the specific task and we will cover this when
we explain how to run the individual tasks.
The report we just defined will be written in the form of a table. So if this is a report for a time course
simulation, the final output would have one line per time step of the simulation and in each line, each object that
is in the list would be written once separated by whatever you defined as your separator character (Normally this
would be the <tab> character).
Per default, the check box labeled Title Row is activated, which means that COPASI will write a header line before
the table with the names of the objects that make up the individual columns. If you don't want such a header in the
output you have to deactivate this check box.
|Advanced Report Definition Dialog
As stated above, the advanced report definition allows you to define the output for the three parts of the report
separately. The header
part of the report is written once before the corresponding task, the output of the
elements occurs once per step of the corresponding task, e.g. for the time course once every time step,
and the footer
is written once after the task has finished. In this sense, the standard table report
definition is nothing but an advanced report definition with a title header and a body that consists of the time and
some species concentrations separated by separator items. The footer is empty. If you write your own advanced report
definition, you are responsible to add separator tags where appropriate. An advantage to the advanced report
definition is that you can add arbitrary text to any of the three sections. Everything else works as described for
the standard report definition, you can add and delete items by selecting them from the object browser dialog. You
can also move these items up and down by selecting them and clicking on the Up or Down button. Separator items can
be added by clicking on the Separator button. The symbol or text that makes up the separator item is again defined
by the check box and the adjacent input field towards the top of the report definition dialog.