This volume, the 7th in the Transactions on Computational Systems Biology series, contains a fully refereed and carefully selected set of papers from two workshops: BioConcur 2004 held in London, UK in August 2004 and BioConcur 2005 held in San Francisco, CA, USA in August 2005.The 8 papers chosen for this special issue are devoted to various aspects of computational methods, algorithms, and techniques in bioinformatics such as modeling of signaling pathways, gene regulation in pi-calculus, relations between regulator graphs and Petri nets, translation of SBML models to stochastic pi-calculus, use of graph theory to model biological networks, distributed model checking with biochemical Kripke structures, graphical notation for stochastic pi-calculus, as well as differentiation and homeostatic behavior of boolean dynamic systems.The Transactions on Computational Systems Biology series is devoted to inter- and multidisciplinary research in computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomen