In the past two decades, multi-agent systems have emerged as a new paradigm for conceptualizing large and complex distributed software systems. Even though there are many conceptual frameworks for using multi-agent systems, there is no well established and widely accepted method for the representation of multi-agent systems. We adapt a well-known formal model, predicate transition nets, to include the notions of dynamic structure, agent communication and coordination to address the representation problems. This paper presents a comprehensive methodology for modeling multi-agents based on the extensions. We demonstrate our modeling approach with an example. Several case studies on di®erent application domains from our previous works are also discussed. Int. J. Soft. Eng. Knowl. Eng. 2012.22:891-925. Downloaded from www.worldscientific.com by CHINESE UNIVERSITY OF HONG KONG on 02/06/15. For personal use only.software engineering community for structuring complex systems running in an open computing environment. Many research activities have been conducted to develop the languages, methodologies and tools for conceptualizing complex systems based on the MAS view. Previous works in this regard were centered on agent-oriented software engineering (AOSE) [25], which focused on the following research topics:(1) requirements engineering; (2) design, speci¯cation and veri¯cation techniques;(3) ontologies; (4) generic agent models and design patterns; (5) validation and testing techniques; and (6) tools to support MAS development. Although the emergence of AOSE is well recognized as a signi¯cant contribution for conceptualizing complex systems based on the MAS architecture, it is still in its infancy towards a mature engineering paradigm to be widely adopted by the software engineering community.In response to the e®orts in developing complex systems based on AOSE, our work aims at speci¯cation and analysis techniques for MAS. The objective is to provide a systematic approach for constructing MAS speci¯cations that can be automatically analyzed at an early stage of system development. Since formal methods provide a sound basis for revealing design°aws, our work is based on model-oriented formal methods [45]. We adopt predicate transition nets (PrT nets) [19] as the underlying formalism to address the representation of MAS. PrT nets are a powerful visual model for studying distributed and concurrent systems. More importantly, PrT nets have precise de¯nitions for operational semantics, which can be manipulated for machine analysis. Nevertheless, PrT nets have a°at net structure that provides only a singlelevel view of the system model, and they are insu±cient in modeling agent communications. To address the shortcomings of PrT nets in modeling MAS, we extended the dynamic semantics of PrT nets to include the notions of dynamic structure, agent communication and coordination. We developed a framework based on our PrT net extensions and developed techniques to facilitate the construction and analysis of MAS models. In summary,...