Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models.

The elevation of Synthetic Biology from single cells to multicellular simulations would be a significant scale-up. The spatiotemporal behavior of cellular populations has the potential to be prototyped in silico for computer assisted design through ergonomic interfaces. Such a platform would have great practical potential across medicine, industry, research, education and accessible archiving in bioinformatics.

Toward Full-Stack Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation.

We present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high-performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates , , , and features into a single software suite.

Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems.

Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations).