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Molecular communication is a new paradigm for communication between biological nanomachines over a short-range (a nano- and micro-scale range). Biological nanomachines are nano- and micro-scale devices that either exist in the biological world or are artificially created from biological materials and that perform simple functions such as sensing, logic, and actuation. Molecular communication provides a mechanism for biological nanomachines to communicate information by propagating molecules that represent the information. Molecular communication is based on observations of existing biological systems which use molecules as communication carriers. With the advancement of current research in areas such as synthetic biology and bio-nanotechnologies, it may become relatively easy in the near future to develop systems of biological nanomachines communicating through molecules. In this paper, we present a framework for describing molecular communication systems.