The Calculus of Looping Sequences (CLS) is a calculus suitable to describe biological systems and their evolution. CLS terms are constructed by starting from basic constituents and composing them by means of operators of concatenation, looping, containment and parallel composition. CLS terms can be transformed by applying rewrite rules. We give a labeled transition semantics for CLS by using, as labels, contexts in which rules can be applied. We define bisimulation relations that are congruences with respect to the operators on terms, and we show an application of CLS to the modeling of a biological system and we use bisimulations to reason about properties of the described system.