As I mentioned in the BioFabric paper, one type of existing visualization where people are used to thinking of "nodes as lines" is the Unified Modeling Language (UML) sequence diagram. There, lifelines are parallel vertical lines that represent objects that are passing messages between themselves in some time sequence. The messages are represented by horizontal lines drawn between the two interacting vertical lifelines. If you rotate the diagram to make the lifelines horizontal, you now have a visualization that would look similar to BioFabric.
But the key difference is that the lifelines are representing objects as they progress though the dimension of time. Of course, representing an object passing through time as a line is a familiar one, perhaps even second nature, for most people. Particularly if the object is a car or a train!
So let's use that insight to provide another way of gaining some intuition about a BioFabric network. Remember that the default layout just uses a breadth-first search of the network, starting at the node with the highest degree (number of incident links); neighbors are visited in the order of their degree as well, highest to lowest.
So think about that search as it proceeds through time, maybe calling out each new link at one-second intervals, so that every second you draw a new link as a "message" between the lifelines of the two nodes. We start drawing the timeline/lifeline for a node when it sends or receives its first message, and stop drawing it when it receives or sends its last message. Thus, a BioFabric network drawing is just a record of this message-passing procedure as it proceeds through time, and we are drawing this step-by-step, with time proceeding left to right. If it helps more, think of the "nodes as points" walking from left to right, one step a second, as they pass these messages:
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| That's a lot of messages between those people marching left to right! |
So if you are having trouble wrapping your head around the BioFabric idea of "nodes as lines", you can always tell Regis that you'd like to use your lifeline!
