title: A generic algorithm for layout of biological networks.
abstract: BACKGROUND
  Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.
  
  
  RESULTS
  We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.
  
  
  CONCLUSIONS
  The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.
authors.affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany. schreibe@ipk-gatersleben.de
authors.forename: Falk
authors.initials: F
authors.lastname: Schreiber
authors.forename: Tim
authors.initials: T
authors.lastname: Dwyer
authors.forename: Kim
authors.initials: K
authors.lastname: Marriott
authors.forename: Michael
authors.initials: M
authors.lastname: Wybrow
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological