Premium
Pathway Preserving Representation of Metabolic Networks
Author(s) -
Lambert A.,
Dubois J.,
Bourqui R.
Publication year - 2011
Publication title -
computer graphics forum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.578
H-Index - 120
eISSN - 1467-8659
pISSN - 0167-7055
DOI - 10.1111/j.1467-8659.2011.01951.x
Subject(s) - computer science , visualization , graph drawing , metabolic network , biological network , context (archaeology) , node (physics) , representation (politics) , graph layout , graph , theoretical computer science , enhanced data rates for gsm evolution , network topology , artificial intelligence , computational biology , computer network , biology , politics , law , political science , paleontology , structural engineering , engineering
Improvements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while respecting biological drawing conventions. These constraints complicate the automatic generation of such visualization as it raises graph drawing issues. In this paper we propose a method to lay out the entire metabolic network while preserving the pathway information as much as possible. That method is flexible as it enables the user to define whether or not node duplication should be performed, to preserve or not the network topology. Our technique combines partitioning, node placement and edge bundling to provide a pseudo‐orthogonal visualization of the metabolic network. To ease pathway information retrieval, we also provide complementary interaction tools that emphasize relevant pathways in the entire metabolic context.