title: An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.
abstract: 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 algorithms, the mapping of nodes to grid points that minimizes a cost function is searched. By imposing positional constraints on grid points, location information including complex shapes can be easily considered. Our layout algorithm includes the spring embedder cost as a component of the cost function. We further extend the layout algorithm to enable dynamic update of the positions and sizes of compartments at each step.
  
  
  CONCLUSIONS
  The new spring embedder-based grid-layout algorithm and a spring embedder algorithm are applied to three biological pathways; endothelial cell model, Fas-induced apoptosis model, and C. elegans cell fate simulation model. From the positional constraints, all the results of our algorithm satisfy location information, and hence, more comprehensible layouts are obtained as compared to the spring embedder algorithm. From the comparison of the number of crossings, the results of the grid-layout-based algorithm tend to contain more crossings than those of the spring embedder algorithm due to the positional constraints. For a fair comparison, we also apply our proposed method without positional constraints. This comparison shows that these results contain less crossings than those of the spring embedder algorithm. We also compared layouts of the proposed algorithm with and without compartment update and verified that latter can reach better local optima.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Japan.
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D000818:Animals; D017209:Apoptosis; D017173:Caenorhabditis elegans / Q000166:cytology; D019295:Computational Biology / Q000379:methods; D042783:Endothelial Cells / Q000166:cytology; D006801:Humans; D008954:Models, Biological