Layout Algorithm

Because pathways and biological networks can be very complicated it is helpful to use graph layout algorithms to reduce visual clutter. VitaPad allows for automatic layout of pathway graphs by means of a built-in "spring-embedded" or "force-directed layout". The algorithm we use is adapted from the GINYproject and was originally based upon an algorithm by Kamada and Kawai.

Basically, this algorithm uses the physical model of a spring to achieve two layout goals:

• Strongly connected elements should be close to one another and should occupy a central location in the graph
• Edge crossings should be minimized

We found this layout to be particularly effective for viewing complex, partially-cyclical graphs such as those for metabolic pathways.