Circuit diagrams for biological networks

Mol Syst Biol. 2: 2006.0002Metabolic maps have long been a staple of biochemistry students, providing clear and concise charts depicting the flow of metabolites and energy in cells. However, depicting the molecular networks involved in signaling pathways that regulate cell function have proven challenging, due to the enormous amount of information that needs to be conveyed for each participant in the network and the cross‐connections between pathways. This challenge must nevertheless be addressed in order to understand the underlying design of such networks, and to utilize the findings of modern biology most effectively to combat diseases, such as cancers, that arise from defects in cell regulation. Another difficulty is that bioregulatory networks are replete with interconnections and loops that make intuition about network function unreliable; therefore, computer simulations may be needed. In a recent issue of Nature Biotechnology , Kitano et al (2005) describe a notation for biological network diagrams, ‘process diagrams’, the formalism of which allows a straightforward conversion of human‐readable diagrams into machine‐readable documents.Hiroaki Kitano and his Symbiotic Systems Project have in recent years focused their attention on bioregulatory networks, how they convey functionality and robustness on biological organisms and how they can be diagrammed and simulated. Kitano (2004) recently reviewed the fascinating field of biological robustness, and insightfully discussed the features that convey robustness to a network. Aiming for a deep understanding …