Integrating software packages for the analysis of biological pathway networks

Interactions at the cellular level are essential for maintaining the fundamental life processes in biological systems. The relationships that are established due to the biochemical reactions occurring within the cells often give rise to extremely complex network structures that may be conveniently represented by bipartite graphs; such networks are often known as biological pathway graphs (BPGs). Given the complexity and size of the resulting graphs, biologists require software tools with advanced visualization and computational capabilities to assist them when performing in-depth structural analysis and hypothesis validation. This paper describes a comprehensive set of Matlab functions (bpg toolbox) for the structural analysis of cell signaling networks represented as BPGs (i.e. into a bipartite graph using a Matlab structure). The toolbox expands the System Biology Toolbox within the Matlab environment by introducing additional functionalities and makes use of Pajek (and GraphViz) which offers numerous advanced graph-theoretic algorithms and excellent rendering capabilities for the analysis of large graphs. The toolbox also supports several standard de-facto formalisms for reaction networks (eg. SBML, CellML). The software is distributed under the GNU License and is freely available at http://ricerca.mat.uniroma3.it/users/strangio. Keywords—biological pathways, bipartite graphs, structural analysis.