An integrated in silico simulation and biomatter compilation approach to cellular computation

t Recent advances in Synthetic Biology are ushering a new practical computational substrate based on programmable information processing via biological cells. Due to the difficulties in orchestrating complex programmes using myriads of relatively simple, limited and highly stochastic processors such as living cells, robust computational technology to specify, simulate, analyse and compile cellular programs are in demand. We provide the INFOBIOTICS WORKBENCH (IBW) tool, a software platform developed to model and analyse stochastic compartmentalized systems, which permits using various computational techniques, such as modelling, simulation, verification and biocompilation. We report here the details of our work for modelling, simulation and, for the first time, biocompilation, while verification is reported elsewhere in this book. We consider some basic genetic logic gates to illustrate the main features of the IBW platform. Our results show that membrane computing provides a suitable formalism for building synthetic biology models. The software platform we developed permits analysing biological systems through the computational methods integrated into the workbench, providing significant advantages in terms of time, and enhanced understanding of biological functionality