Version 0.79, October 2006

This guide shows how to use the Graphical User Interface for the SBW AutoLayout Module.

All clickable menu items and buttons (or their associated keystrokes) will be in italics.

To open an SBML File:

1. Drag and drop the file onto the SBW AutoLayout window, OR
2. Select File > Load SBML File or press CTRL-O. You can then browse and select the file to open.

If the SBML file has layout information, the model will be displayed as specified by its layout. If the model does not have layout information, SBW AutoLayout will generate all necessary data for saving the model with layout information.

To save an SBML File:

1. Select File > Save SBML File or press CTRL-S. You can then browse to where you would like to the save the file and specify the file name.

Images of the full network or a screenshot of the network can be saved. Full network saves the whole network, regardless of what is visible in SBW AutoLayout's window. Screenshot saves only what is visible in SBW AutoLayout's window. To save an image of the full network:

1. Select File > Save Image > Full Network or press CTRL-SHIFT-S. You can then browse to where you would like to the save the file and specify the file name.
2. Select the format for the image: PNG, BMP, JPG, or PS

To save an image of a screenshot:

1. Select File > Save Image > Screenshot. You can then browse to where you would like to the save the file and specify the file name.
2. Select the format for the image: PNG, BMP, or JPG

Note:

• PNG, BMP, and JPG images are raster formats. They are good for including the files in other electronic media, but are not high enough quality for printing or making the images larger.
• PS is a vector format. This format allows the images to be resized and printed with high quailty.

The SBW menu allows users to transfer models between SBW-enabled applications without importing/exporting the models between programs.

1. To send models from SBW AutoLayout, load a model into SBW AutoLayout and select another program from the SBW Menu. The model will be sent to other program.
2. To send models to SBW AutoLayout, select SBW AutoLayout from the SBW Menu in another program.

Panning is the movement of the drawing canvas on the screen in horizontal and/or vertical directions. This allows for visually exploring even large models. To pan on the canvas:

1. Left mouse click on an empty part of the canvas
2. Hold and drag the canvas in any desired direction
3. Release the mouse button

Zooming makes the model larger or smaller on the screen. To zoom:

1. Roll the mouse scroll outward to zoom out
2. Roll the mouse towards inward to zoom in

Compartments are defined in the SBML for the model. The topmost (default) compartment is always hidden, but all other compartments can be hidden or shown. While the forces and control points cannot be directly manipulated, they show how the program is positioning the models. The forces shown are the springs for the connections and the repulsion that occurs in the middle of the connections, however the forces associated with the nodes are simply their size. These are used by the layout algorithm to adjust distances between nodes. Control points are used to set the curves for the model’s connections. To change their visibility:

1. Under the View menu, click on Show (Compartment, Forces, Control Points) to toggle the item's visibility.

Fit On Screen automatically moves (pans) and sizes (zooms) that the whole model will be displayed on the screen. To do this:

1. Select View > Fit On Screen or press F5.

To find and center a particular node on the screen (without adjusting the zoom):

1. Click the selection box labeled Center Node below the canvas
2. Select the node (species) to be centered from the list of all available species

Within SBW AutoLayout, the cursor has three different modes:

• Select Element - Used to select and move nodes and connections
• Lock Element - Used to lock nodes and connections
• Alias Node - Used to alias (make copies for each connection) a node

To change the cursor mode:

1. Right mouse click on the canvas (where the model is displayed) and select the preferred mode from the drop down list.

Dragging nodes and connections allows for adjusting the network layout. When nodes and connections are moved, the curves for the connections are automatically recalculated to maintain their coherence. To move these elements, the cursor must be in the Select Element mode. To drag a node:

1. Left mouse click on a node
2. Hold and drag the node in any desired direction
3. Release the mouse button

To drag a connection:

1. Left mouse click on the connection marker (a light purple circle) in the center of the connection
2. Hold and drag the connection in any desired direction
3. Release the mouse button

Locking nodes and connections keeps them from being moved during automatic layout. To move these elements, the cursor must be in the Lock Element mode. To lock a node:

1. Left mouse click on a node
2. The color of the node will darken to indicate it is locked

To lock a connection:

1. Left mouse click on the connection marker (a light purple circle) in the center of the connection
2. The color of the connection marker will darken to indicate it is locked

Aliasing a node creates copies of the node for each connection that was attached to the node. These nodes have the same text as the original node and are then shown with a dotted line around them. Nodes can be aliasing individually by selecting the Alias Node Cursor, or all nodes with a specified degree or higher can be automatically aliased. To alias a single node, the cursor must be in the Alias Node mode.

1. Left mouse click on a node
2. Alias nodes will appear

To alias multiple nodes based on their degree:

1. Use the controls at the bottom of the window labeled Auto Alias Nodes
2. Select a degree; all nodes with this degree (number of connections touching it) or higher will be aliased
3. Click the alias button
4. Alias nodes will appear, and the number of nodes that were aliased and the number of alias nodes that were created will be displayed in the bottom right corner of the window

NOTE: when aliasing nodes, the program will not alias any nodes that may disconnect the network

Any moving, aliasing, or layout performed on the network can be undone or redone. Undo removes whatever action was last performed on the network. Redo can only be used after Undo to remove the changes made by Undo. If the model is manipulated after using Undo, the option to use Redo is not longer available. Both of these can be used repeatedly.

1. To Undo, select Edit > Undo or press CTRL-Z
2. To Redo after an Undo, select Edit > Redo or press CTRL-Y

Randomizing places all the nodes and connections into randomly selected positions. To Randomize the loaded model:

1. Select Edit > Randomize or press F7

The basis for this algorithm is force-directed placement (Fruchterman, T. M. J. and Reingold, E. M., (1991) Graph drawing by force-directed placement. Software, Practice and Experience, 21, 1129-1164.). The model is treated as a physical system, where the nodes are treated as repulsive particles and the connections act as springs with an optimal distance. The springs attempt to attain their optimal distance by pulling connected nodes together that are too far apart, or pushing connected nodes apart that are too close together. This system of springs and repulsive nodes are then then simulated until they reach a relatively stable configuration.

Automatic Layout moves all the nodes and connections in a loaded model to make a readable visualization of the model. To perform Automatic Layout:

1. Click the Layout button on the bottom left corner of the window, select Layout > Auto Layout, or press F6

The following parameters can be adjusted:

• Node Spacing - the optimal distance between the nodes
• Gravity - acts to pull together all nodes and connections to a central point

The following parameters can be turned on or off:

• Magnetism - acts to align connections so that all reactants are drawn together and all products are drawn together
• Boundary (experimental) - attempts to contain the network within a set space (currently calculated by the program)
• Grid (experimental) - attempts to place the nodes in the network in an orderly grid

Node spacing controls the preferred distance between the nodes. Gravity controls how strongly all elements in the model are attracted to a central point. Gravity is most useful for keeping disconnected models together and for wrapping long models

• Node spacing is controlled by a slider at the bottom of the window.
  • Moving it towards the ”-” sign makes the space between the nodes less.
  • Moving towards the ”+” sign makes the space between the nodes greater.
• Gravity is controlled by a slider at the bottom of the window.
  • Moving it towards the ”-” sign makes the gravity less and lets the elements in the model spread further apart.
  • Moving towards the ”+” sign makes the gravity greater and keeps the elements in the model closer together.

alias
Making identical copies of a node for each of the node’s connections. Each copy is called an alias of the original node. This allows the alias nodes, and the associated connection, to be moved separately from the original node, which allows for simplifying the layout of the model.

canvas
The canvas is the white square that occupies most of SBW AutoLayout’s window, and the models are drawn on the canvas. The canvas can be manipulated by panning, which moves the models, or zooming, which resizes the models.

control points
Points that control the curves for the reactions. These are usually hidden.

gravity
A force that acts to pull all the parts of the model towards a common center. This helps to keep disconnected or long, stringy models compact.

magnetism
A force that acts to keep the arrows indicating the direction of reactions aligned when there are several products or reactants. It works by attracting reactants to reactants and products to products, while repulsing reactants from products.

springs
Forces between the nodes used by the layout algorithm to adjust distances between nodes. These are usually hidden.