In the pathway window, click-and-drag to draw a line from a first node to a second. When you let go of the mouse button, a process is created connecting the two nodes.
- The starting node is a reactant.
- The ending node is a product.
- A small process icon is is drawn mid-way between the two nodes.
- Arrows connect the nodes to the process icon

You can add more nodes into the process by adding more connections.

All new processes are gray and use simple arrows. You can set the process type to change the line color, and set node roles to change how arrows are drawn.

Adding more connections to a process

A process can have connections to any number of nodes.

Enter connection-drawing mode by pressing the arrow-shaped button on the toolbar at the top of the pathway window.

Add a process or use an existing process.
In the pathway window, click-and-drag to draw a line from a node to the process icon, or from the process icon to a node.
- If you start on a node and end on a process icon, the node is a reactant.
- If you start on a process icon and end on a node, the node is a product.

You can set node roles in the process.

Selecting a process

Select a process in a pathway:

In the pathway window, click on a process' icon. The process is highlighted with a thick border around it.

Once selected, you can delete the process and get process information where you can change the process's name, set node roles in the process, or set node stoichiometry, etc.

Selecting a connection in a process

Select an individual connection in a process in a pathway:

In the pathway window, click on a line drawn between a node and a process' icon. The line is highlighted with a thick border around it.

Once selected, you can delete the connection and get process information where you can change the process's name, set node roles in the process, or set node stoichiometry, etc.

Deleting a process

Delete a process from a pathway:

Select a process .
Delete it by doing one of the following:
- Press the DEL key on your keyboard.
- Press the BACKSPACE key on your keyboard.
- Select "Delete" from the "Edit" menu.
- Right-click on the node to show a pop-up menu and select "Delete".
The deleted process is removed from the pathway.

Deleting a connection in a process

Delete a connection in a process in a pathway:

Select a process connection.
Delete it by doing one of the following:
- Press the DEL key on your keyboard.
- Press the BACKSPACE key on your keyboard.
- Select "Delete" from the "Edit" menu.
- Right-click on the node to show a pop-up menu and select "Delete".
The deleted connection is removed from the pathway.

Moving a process

Move a process within a pathway:

In the pathway window, click-and-drag the process' icon to move it around. If the process is connected to any nodes, the connections move with the process.

A "click-and-drag" is done by pressing the left mouse button down atop the process icon, then draging the mouse about while holding down the button. When you let go of the mouse button, the process icon stops moving.

Getting process information

The process information window shows the process's label, type, and node role information.

In the pathway window do one of the following:
- Select a process or select a process connection, then choose "Show process info..." from the "Edit" menu.
- Double-click on a process icon.
- Right-click on a process icon to show a pop-up menu and select "Show info...".

Setting a process label

Every process as a label shown in the process list, but not in the pathway drawing. Change the process' label:

Get the process information window for the process you want to change.
Type a new name into the box labeled "Label:".

Assigning a process type

A process' type determines it's color on the pathway drawing. You can assign a process type:

Get the process information window for the process you want to change.
Select the process' type from the pull-down menu labeled "Type:". There are large number of types, including those typically used for metabolic or signaling pathways.

Setting node roles in a process

You can change the role each node has in a process:

Get the process information window for the process you want to change.
Click on the "Nodes" tab. The tab lists the nodes in the process.
In the "Role" column, select the role for the node you wish to change. There are several node roles, including those typically used for metabolic or signaling pathways.

Setting node stoichiometry in a process

You can change the stoichiometric constant of each node in a process:

Get the process information window for the process you want to change.
Click on the "Nodes" tab. The tab lists the nodes in the process.
In the "Stoichiometry" column, click and type in a new stoichiometry value. Values must be numbers greater than 0.

Adding comments

You can add your own comments about a process:

Get the process information window for the process you want to change.
Click on the "Comments" tab and type text into the box below.

Listing processes

You can get a list of all processes in a pathway:

In the "Tools" menu, choose "Manage processes...". This presents a window showing a list of the pathway's processes.

Select a process and press the "Show info..." button to show the process' information window.
When you are done with the window, press the "Done" button.