Joint work with Vincent Danos (Laboratoire Preuves Programmes et Systèmes,CNRS, France), Jerome Feret (Ecole Normale Supérieure, Paris), Walter Fontana (Systems Biology Department, Harvard Medical School, US).
In this talk we present Simplx, a tool currently in development at Plectix Biosystems (Boston, US) allowing to analyse and simulate large bio molecular systems. The tool relies on an agent based formalism called the kappa-calculus . We first present the kappa-calculus in which states, called solutions or systems, are graphs where connections are made on sites and transitions are generated by a restricted class of graph-
rewriting rules. We will then proceed with the technical description of Simplx features.
 Formal Molecular Biology (TCS 325, 2004) Vincent Danos, Cosimo Laneve.