In recent years, the increasing importance of the computational systems biology is leading to an impressive growth of the knowledge of several real-life phenomena. In this framework, membrane computing is an emergent branch within natural computing that has been successfully used to model biological phenomena. The study of these phenomena usually requires the execution of virtual experiments using mechanisms of simulation, implying the development of ad-hoc tools to simulate. However, the advance of the research is demanding general solutions to avoid the necessity of custom software developments for each matter of study, when there are some common problems to resolve. MeCoSim (Membrane Computing Simulator) is a first step in this direction providing the users a customizable application to generate custom simulators based on membrane computing by simply writing a configuration file.