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This work presents a new methodology known as Activity-Oriented Petri Net (AOPN). AOPN is designed for modeling discrete systems where many activities compete for common system resources. AOPN let resource management issues to be handled by the underlying system in the background so that modelers can focus on modeling the activities, rather than on the resource management trivialities. By the AOPN methodology, allowing the resources managed by the underlying system provides much simpler models even for large and complex systems. Thus, the models become easy to understand, verify, and to conduct performance analysis. General Purpose Petri Net Simulator (GPenSIM) is a toolbox of functions that realizes AOPN methodology on MATLAB platform. In this work, the AOPN methodology and GPenSIM is described through a case study that involves modeling resource management for a software development project.