Genetic engineering has developed around technologies enabling the targeted in vitro recombination of DNA molecules found in living organisms. As a result, the development of new DNA molecules has been primarily focused on cloning strategies that allow their assembly from existing DNA fragments. As chemical gene synthesis matures, the design of synthetic DNA molecules becomes the bottleneck of many biotechnology projects. It becomes urgent to develop representations of synthetic genetic systems more than their DNA sequence. ion makes it possible to reuse simple components to build complex systems or to break down a complex engineering problem into manageable tasks. Specialized computer languages or a general purpose XCell Description Language are promising avenues to build ion hierarchies for synthetic biology.