Designing synthetic communities with organism-free modular computational models


Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It has reached a maturity level that enables construction of artificial communities of synthetic organisms. Considering the strong engineering component in synthetic biology design, we highlight the role of computational models in reaching the full potential of this emerging field. Computational models have been shown to be an essential part of biology entangling the nonlinearly increasing complexity with the growing number of components, and emerging properties of biological phenomena. In recent years, great hope has been put in modelling efforts to guide synthetic biology approaches in much the same way as they guided engineers to design new technical devices. Yet, till now, modelling has not been fully integrated into the synthetic design process. Here we summarise the state of the art and discuss how synthetic biology design can be supported with an organism-free modular modelling approach focussing on designing synthetic multi-species communities. We argue that efforts should shift from organism- and context-specific complex systems or even whole-cell models to modular computational models with mathematical descriptions of parts and circuits, from which synthetic systems could be systematically assembled. Such an approach would be more compatible with synthetic biology approaches, opening the door to designing artificial communities.