D-VASim: Dynamic Virtual Analyzer and Simulator for Genetic Circuits

A genetic circuit represents a gene regulator network that is triggered by a combination of external signals, such as chemicals, proteins, light or temperature, to emit signals to control gene expression or metabolic pathways accordingly. In order to match the intended behaviour, genetic circuits are either assembled from a standard library of well-defined genetic gates or from parts of an available library, for instance, BioBricks.

The obtained behavior can be validated through in-silico analysis, solving reaction kinetics using ordinary differential equations (ODEs) or by stochastic simulation, with the aim to reduce the number of required in-vitro experiments. We present a behavioural simulation and analysis tool that allows the biologist to carry out virtual lab experiments as an interactive process during simulation of the genetic circuit, rather than a batch process, which is current practice.

We believe that this increases the insights gained from the analysis and allows for exploring more parameters in an intuitive manner.