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

YesComputational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems.EPSR

Modelling and stochastic simulation of synthetic biological Boolean gates

NoSynthetic Biology aspires to design, compose and engineer biological systems that implement specified behaviour. When designing such systems, hypothesis testing via computational modelling and simulation is vital in order to reduce the need of costly wet lab experiments. As a case study, we discuss the use of computational modelling and stochastic simulation for engineered genetic circuits that implement Boolean AND and OR gates that have been reported in the literature. We present performance analysis results for nine different state-of-the-art stochastic simulation algorithms and analyse the dynamic behaviour of the proposed gates. Stochastic simulations verify the desired functioning of the proposed gate designs

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