Nowadays, in order for a company to remain competitive, efficient and attractive to investors it needs to have reliable and threat-resistant business processes. The question of methods for building such business processes remains relevant. This paper proposes a software system, which involves the use of methods and tools of DSM (Domain Specific Modeling), ontological approach, simulation modeling methods, mass service theory, Petri nets. As an example, the logistics process of ship boarding in the port is considered. Software tools implementing simulation modeling and DSM are ANYLOGIC and METALANGUAGE.