Links are used to transfer data (signals) from one node to another. Both directed links ( and i ) have the same functionality as the simple link ( | ), but the negated link ( ^ )'negates' the data it transfers. The exact transformation depends on the function of receiving symbol, and will be explained in more detail later.
In general, symbols are linked by pressing one of the link buttons, which changes the cursor into a cross (the Creating link cursor) when it is over the canvas, and into a cross inside a circle when the cursor is over a post that will accept the connection (the Accept link cursor). A connection between a link and a symbol is made by single clicking the left mouse button when the Accept link cursor is visible. To make a connection to another symbol, move the cursor (now in the Creating link state again) over the other symbol, until the cursor hits the port that you want to make the connection to and changes into the Accept connection cursor (if it fails to do so, there is no port, or the connection is forbidden). Single left clicking will then connect the other end of the link.
Some more things to know about link creation:
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A link can be selected in the same way as node and cell symbols. |
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Single right clicking during dragging will abort the link creation process. |
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When you are dragging an unfinished link and do a single left click, a vertex will be created at the point where you clicked. |
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Double click during dragging: the link will be terminated, with one end unconnected. The link is now represented by a dotted line, to indicate it is not fully connected. Links that are not connected at one or both ends have no function, and need to be deleted before you can start a simulation. |
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You can reconnect a link by picking up its unconnected end (select the link, move the cursor over its unconnected end, click when it changes into a small square with arrowheads protruding from all sides), and dragging to an appropriate port whilst holding the left mouse button down. |
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If you delete or cut and paste a symbol, all of its links will need to be reconnected. |
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Right clicking on an existing link will bring up the popup menu that gives access to the link’s properties. |
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Left clicking an existing, selected link somewhere on its line while the Ctrl key is pressed will create a new vertex at the point where you clicked, and when you click on an existing vertex while the Ctrl key is pressed, the vertex will disappear. |
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Creation of directed links (all links apart from the one created upon the Simple Link command) must start at an output port, creation of a Simple Link can start at either type of port. |
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When the create link command has been given, the canvas will scroll automatically when the cursor is over one of its borders. If the canvas starts scrolling wildly for reasons not immediately apparent to you, chances are that you intended to create a link, and then forgot about it. Move the cursor onto the canvas, and right click to stop the process. |
Link the symbols as indicated in the figure. Note that the input links to the And and Or functions stop at the symbols perimeters, but are actually are connected to the input port in the centre of the circle. As mentioned above, the choice between simple and directed links is made on aesthetic grounds.
Notice that the input and output ports 0 on the General Gene symbol (at the bottom and tip of the arrowhead of the bent arrow) have a function that is different from the other ports. Input port 0 takes the result of the function sequence that specifies the effect of the TF interactions with the cis-regulatory domain, and output port 0 presents the overall gene output to the rest of the network.
'All And' and 'All Or' genes are equivalent to General Genes in which all input ports are connected to an And or an Or function:
However, in the case of the 'All And' and 'All Or' genes, their input ports 0 are equivalent to their other input ports, and can be used in the same way, if required.