This is a brief tutorial for the beta 2 Pathway Editor.
Click on Pathway Editor to start the application. Click on "yes" each time you are asked if you trust our downloads (we assume you do).
When the download completes, the editor will start up and look like this:
Go to the "File" menu and select "Open pathway database ..." to show a search window:
By default, the search looks for all pathways of any type. Constrain the search by typing a keyword and/or selecting a pathway type. Click "Search" to search the database for matching pathways.
Select the "Arachidonic acid" pathway and press the "Select" button. The pathway will load:
Go to the "File" menu and select "Open pathway file..." to get a file-opening window. Select a file, click "Open" and the pathway will load.
Go to the "File" menu and select "New pathway " to create a new empty pathway.
The pathway editor is similar to a drawing application. On the toolbar, select the box-shaped icon (2nd from left), then click in the main area to drop a new node at the cursor. Nodes are always box-shaped icons.
The blue outline shows the node is selected.
You can show information about a selected node by doing any of the following (they are all equivalent):
All of these bring up a window about the node. From this window you can change the node's label, compound, and other attributes.
To assign a compound to the node, select the "Compound" tab and press the "Select compound..." button. This shows a compound search window.
Constrain the search by selecting the compound type and category and/or entering a keyword. Then press "Search" to get a list of results.
Select one of the compounds from the list and press the "Select" button. The compound is loaded from the database and assigned to the node. You can view the compound's details by pressing the "Show info..." button on the node's information window.
Change the node's label to anything you want by typing a new value in the "Label:" box in the node's information window.
This changes the label on the node's box in the main drawing area.
Continue using the "box" icon and drop some more nodes into the pathway and assign them compounds.
Click on the dot-and-arrows icon on the toolbar (third from the left) and click-and-drag to draw connections between nodes.
A process is a connection between two or more nodes. The process is drawn as a dot and arrows connecting the dot to nodes. Nodes with arrows into the dot are reactants. Nodes with arrows from the dot are products.
The first time you connect two nodes, you create the process. After that, you can drag a connection from a node to the dot, or from the dot to a node to add the node to the process.
You can show information about a process by selecting the process dot and then:
All of these show an information window about the process.
From this window you can label the process, change its process type, and see a list of the nodes connected to the process. For each of these nodes, you can change their role in the process and their stoichiometry. A node's role can be a reactant, a product, a catalyst, an inhibitor, and so on. Inhibitor nodes are drawn with a "bar" on their connection line. The rest are shown with arrows.
Click on the arrow icon on the toolbar (the left-most button). Click and drag to move any node. Process arrows stay attached. Click and drag a process dot to move the dot.
Shift-click to select multiple nodes. Or click on the background and drag open a selection box around nodes and processes to select a group, then move them as a group.
Go to the "File" menu and select "Save pathway as..." to get a save window. Enter a file name, select the "PATH" file type and click "Save." The PATH format is our own file format that supports saving all the data in a pathway.
Go to the "Tools" menu and select "Manage experiments..." to get a list of loaded experimental data (initially empty).
Click on the "Add" button to add an experiment from the database.
Optionally enter a keyword and press the "Search" button to search the database.
Select an experiment from the list and press the "Select" button to load it into the pathway. Relevant experimental data is automatically shown in little plots under each node in the pathway.
To view an experiment's data, select the experiment and press the "Show info..." button.
Select any of the compounds in the experiment's window to show their plot and raw data to the right.
You can add more experiments in the main experiment window by clicking the "Add" button and searching the database again. Click the "Remove" button to remove an experiment. Click on the checkbox beside an experiment to show it in the pathway (checked) or hide it (unchecked).