We introduce a framework for the development of modular lumped and distributed parameter system models, the latter described by boundary value problems. The simulation of such systems requires careful analysis and a rigorous approach to development to provide both accuracy and computational efficiency. We explain the current implementation, which solves such systems in a MATLAB environment using object-oriented programming principles as part of the Modular Distributed Parameter System Analysis and Simulation (MDPSAS) package. We propose a mechanism for creating user-defined simulation elements using a web-based collaborative interface. The creation of a novel semantic vocabulary built into an XML application language called ModSimML is presented as a tool for data structuring and exchange. The development of a schema for the XML application formalizes of our data model. The utility of this interface is described via an application to research in Biological Micro-Electro-Mechanical Systems (BioMEMS), whose simulations require assembly from modular components.