Compartmental Scheme Windows

You construct, modify and operate on Kinetiscope's reaction schemes using scheme windows. Each scheme window includes a Scheme Page tailored for its particular type of reaction scheme.

The Scheme Page of a compartmental scheme window looks like this:

This page contains a scheme diagram of the reaction scheme. On the scheme diagram, compartments are represented by labeled rectangles and transfer paths are represented by labeled arrows. You may also add text annotations to the scheme diagram.

Above the scheme diagram is a tool bar with a row of push buttons that allow you to add, remove and edit compartments and transfer steps, start a simulation of the reaction scheme, or create a new results window, a separate window that presents the output of the last simulation.

A single click of the right mouse button in an empty area of the scheme diagram displays a context menu listing more available actions.

The current status of the reaction scheme is indicated by the status bar along the bottom of the window.

Creating a Compartmental Scheme

To create a new compartmental reaction scheme:

1. Select File | New Scheme | Compartmental Model... from the main menu of Kinetiscope's main window, or click the push button on the main window's tool bar.

   A Select Units Dialog appears.

2. Using the Select Units Dialog, choose the units you wish to use.
3. Click the OK push button on the Select Units Dialog.

A new compartmental scheme window whose scheme diagram contains a single empty compartment is added to Kinetiscope's main window.

You now use the tool bar and context menus to construct and configure the reaction scheme.

Using the Tool Bar

For a number of the tool bar's push button actions, you first select one of the objects in the scheme diagram within the scheme display area and then click the selected tool bar push button.

To select an object:

• Single-click the object with the left mouse button.
The selected object appears cross-hatched to indicate its state.

The push buttons and their functions are as follows:

Add a new transfer path.

Clicking this push button initiates the addition of a new transfer path between two compartments. The mouse cursor becomes a cross.

To complete the addition of a new transfer path:

1. Press and hold down the left mouse button while over the first compartment (the source);
2. While holding down the mouse button, move the mouse cursor to the second compartment (the target); a "rubber-band" line follows the cursor movement.
3. Release the mouse button while the cursor is over the second compartment. The rubber band line is replaced with a new, labeled transfer path.

You may now edit the new transfer path.

To Edit a transfer path:

• Double-click the transfer path with the left mouse button
or
• Select the new transfer path as desribed above, then Click the (Edit) push button (see below).
Either action opens the Transfer Path Editor Dialog where you may specify transfer steps and their parameters.

The designations of source and target are arbitrary; this simply determines the meaning of "forward" and "reverse" when entering rate parameters for a transfer step added to the transfer path.

The scheme diagram must have at least two compartments for this button to be active.

Add a new compartment.

Clicking this push button inserts a new compartment near the center of the scheme diagram.

You may drag the new compartment to a different location by pressing and holding down the left mouse button while over the compartment, then dragging it to the new site. Release the left mouse button to anchor the compartment there. Compartments may be relocated this way at any time. When moving a compartment, all transfer paths maintain their connections.

You may now edit the new compartment.

To edit a compartment:

• Double-click the compartment with the left mouse button
or
• Select the new compartment as described above , then click the (Edit) button (see below).
Either action opens the Compartment Editor Dialog where you may specify reaction steps, species concentrations and other parameters.

Add a new annotation.

Clicking this push button inserts a new text annotation in the upper-left area of the scheme diagram. You may then move, edit, change text attributes and delete the annotation.

Copy the selected object.

When this push button is clicked, a copy of the currently selected object is placed on Kinetiscope's internal clipboard. That copy may be pasted into this reaction scheme, or into another reaction scheme that is loaded into memory.

Paste an object.

This push button is only enabled when a valid compartment, transfer step or annotation is on Kinetiscope's clipboard from a previous Cut/Copy action.

The action taken depends on whether an object in the scheme diagram is selected:

• If the selected object is the same type as the clipboard object, then the selected item in the scheme diagram is replaced with the copy on the clipboard.
• If the selected object's type is different from the clipboard object, then no action takes place.
• If no object is selected, then the Paste operation adds a new object to the scheme diagram, of the same type as the object on the clipboard.

If you are pasting a transfer path, then the cursor becomes a cross and you indicate the source and target compartments as described earlier.

Cut the selected object.

This action deletes the selected object from the reaction scheme and places it on Kinetiscope's internal clipboard. It may be pasted into this reaction scheme, or into another reaction scheme that is loaded into memory.

When you cut a compartment, all transfer paths connecting to it are deleted.

Delete the selected object.

This action deletes the selected object from the reaction scheme and discards it.

When you delete a compartment, all transfer paths connecting to it are deleted.

Edit the selected object.

This action opens the appropriate editor dialog for the selected object. This same action may be initiated by double-clicking the left mouse button on the object.

Search the scheme for species usage.

This action searches for usages of a species you specify. When triggered, an initial menu allows you to choose whether you want to search in all compartments, all transfer paths, or in a subset of these objects you have previously selected. A Search Objects Dialog then appears where you can specify search critera and scan the objects.

Zoom in.

This action increases the scale of the scheme diagram. You may also zoom in and out using the mouse wheel.

Zoom out.

This action decreases the scale of the scheme diagram. You may also zoom in and out using the mouse wheel.

Zoom to full scale.

This action resets the scale of the scheme diagram to its original scale.

Zoom to show all.

This action sets the scale of the scheme diagram to ensure all objects are visible.

Create a new simulation results window.

This push button is only enabled when a simulation has been successfully run and simulation results are available.

To create a new results window:

1. Select a compartment to be plotted as described above.
2. Click this button.

A new line plot window s created in the main window's workspace. That window initially displays a plot of the concentrations of all species as a function of time for the selected compartment. You may then modify the view to display other parameters.

Start a simulation.

When this push button is clicked, Kinetiscope performs some internal tests of the reaction scheme to ensure that the simulation will start successfully.

If these tests are successful, a simulator window opens and Kinetiscope starts the calculation. The current reaction scheme is locked to prevent editing during the simulation, but you may continue to work with other reaction schemes while simulations are in progress.

If the reaction scheme fails one of the pre-simulation tests, a message box appears to notify you of the issue.

Context Menus

For each object in the scheme diagram, you may display a context menu by single-clicking the right mouse button over the object. See the detailed descriptions of compartments, transfer paths and annotations for more on their menus.

The scheme diagram itself has a context menu, displayed by single-clicking over any empty area in the scheme diagram. This menu can initiate the actions listed here:

The first eight entries provide an alternate means of triggering the functions already assigned to the tool bar buttons. The remaining four actions are

Lock the Scheme Layout

selecting this menu item toggles a lock on the layout of the scheme diagram.

When locked, the positions of all the objects are fixed. The locked state is indicated by a check mark. The locked state is preserved when the reaction scheme is saved to a file.

Copy Diagram Image to Clipboard

When this menu item is selected, a bitmap image of the scheme diagram is placed on the system's clipboard.

This image may be pasted into other applications.

Export Diagram Image to File...

When this menu item is selected, a File Save Dialog appears that allows you to save an image of the scheme diagram to a disk file.

The image is saved in Portable Network Graphics (.png) format.

View Text Listing of Reaction Scheme...

This menu item opens a new Show Text Listing Dialog displaying all details of the reaction scheme.

Selecting Objects in the Diagram

You must select compartments or transfer paths when using copy-and-paste operations to construct your reaction scheme.

Two different methods for selecting objects are available in a compartmental reaction scheme:

Selection using the Mouse

To select one or more compartments or transfer paths:

1. Press and hold the left mouse button while resizing the rubber-band box that appears so that it contains the desired items.

   The selected items are highlighted with a cross-hatched pattern while you resize the rubber band box.

2. Release the left mouse button and the items remain selected.

The type of item selected depends on the type of object most recently placed on the clipboard. If a compartment is on the clipboard then only compartments in the diagram are selected; if a transfer path is on the clipboard then only transfer paths are selected.

To clear a selection:

• Click the left mouse button on any empty area of the scheme diagram.

Selection using the Compartment Context Menu

Each compartment has Selection sub-menu accessed by choosing the Select... menu item from its context menu. On compartmental reaction schemes, that Selection sub-menu lists the following selection options:

You may use these actions to select multiple objects. When you select using one of these actions, the selected objects are indicated by crosshatching.