A layout algorithm for signal transduction pathways as two-dimensional drawings with spline curves

Abstract

As the volume of the biological pathway data is rapidly expanding, visualization of pathways is becoming an important challenge for analyzing the data. Most of the pathways available in databases are static images that cannot be refined or changed to reflect updated data, but manual layout of pathways is difficult and ineffective. There has been a recent interest in the use of the three-dimensional (3D) visualization for signal transduction pathways due to the ubiquity of advanced graphics hardware, the ease of constructing 3D visualizations, and the common perception of 3D visualization as cutting-edge technology. However, our experience with visualizing signal transduction pathways concluded that 3D might not be the best solution for signal transduction pathways. This paper presents an algorithm for dynamically visualizing signal transduction pathways as 2D layered digraphs. © Springer-Verlag Berlin Heidelberg 2005.