Background: Linking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large...
Ming Jia, Suh-Yeon Choi, Dirk Reiners, Eve Syrkin ...
Background: Standard graphs, where each edge links two nodes, have been extensively used to represent the connectivity of metabolic networks. It is based on this representation th...
Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabili...
Jan Schellenberger, Junyoung O. Park, Tom M. Conra...
Abstract. Metabolic P systems, shortly MP systems, are a special class of P systems, introduced for expressing biological metabolism. Their dynamics are computed by metabolic algor...
—This paper describes a new logic-based approach for representing and reasoning about metabolic networks. First it shows how biological pathways can be elegantly represented in a...