A graph layout algorithm for drawing metabolic pathways

A graph layout algorithm for drawing metabolic pathways

MOTIVATION A large amount of data on metabolic pathways is available in databases. The ability to visualise the complex data dynamically would be useful for building more powerful research tools to access the databases. Metabolic pathways are typically modelled as graphs in which nodes represent chemical compounds, and edges represent chemical reactions between compounds. Thus, the problem of v...

Comparison of Metabolic Pathways using Constraint Graph Drawing

Databases contain a large amount of data about metabolic pathways, in particular about similar pathways in different species. Biologists are familiar with visual representations of metabolic pathways. Visualizations help them to understand the complex relationships between the components of the pathways, to extract information from the data, and to compare pathways between different species. Ho...

A New Constraint-Based Compound Graph Layout Algorithm for Drawing Biochemical Networks

Due to the huge amount of information available in biochemical databases, biologists need sophisticated tools to accurately extract the information from such databases and to interpret it correctly. Those tools must be able to dynamically generate any kind of biochemical subgraph (i.e., metabolic pathways, genetic regulation, signal transduction, etc.) in a single graph. The visualization tools...

An Algorithm for Drawing a Graph Symmetrically

A technique is described that produces symmetric drawings of a graph G in the plane. The method requries that G have a non-trivial automorphism group Aut(G), and that a non-trivial symmetry g ∈ Aut(G) has been selected in some way. The technique is found to be very effective in practice. It forms a part of the Groups & Graphs** software package. 1. Symmetric Cycles Let G be a connected undirect...

An Algorithm for Drawing a Hierarchical Graph