An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location inf

Background: Graph drawing is one of the important techniques for understanding biological regulations in a cell or among cells at the pathway level. Among many available layout algorithms, the spring embedder algorithm is widely used not only for pathway drawing but also for circuit placement and www visualization and so on because of the harmonized appearance of its results. For pathway drawing, location information is essential for its comprehension. However, complex shapes need to be taken into account when torus-shaped location information such as nuclear inner membrane, nuclear outer membrane, and plasma membrane is considered. Unfortunately, the spring embedder algorithm cannot easily handle such information. In addition, crossings between edges and nodes are usually not considered explicitly. Results: We proposed a new grid-layout algorithm based on the spring embedder algorithm that can handle location information and provide layouts with harmonized appearance. In grid-layout ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Kaname Kojima, Masao Nagasaki, Satoru Miyano
• Keywords: Algorithm, BMCBI 2010, Layout Algorithm, Spring Embedder Algorithm