D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits

Abstract

haba@dtu.dk, jama@dtu.dk.

Taming Living Logic Using Formal Methods

“…The threshold level of a genetic circuit can be defined as the minimum concentration of input protein(s), which causes the average concentration of output protein to cross the level of input protein(s) concentration [40]. D-VASim [39] is a simulation tool which supports the capability of analyzing the threshold value and timings of genetic circuits through an automated process. It further allows the user to perform runtime interactive simulations.…”

“…Similar to the electronic design automation (EDA) process which dramatically enhanced the design, verification, validation and production of electronic circuits, researchers have started to work on the development of genetic design automation (GDA) tools to automate the design, test and verification processes of genetic circuits prior to their validation in laboratory. Several computational tools [31][32][33][34] have been developed to assist users in the model construction and design [35][36][37], simulation [35,36,[38][39][40], logic and timing analysis of genetic circuits [40], and model checking [36,[41][42][43][44]. Model checking of biological systems is getting popular as it is an effective means of analyzing the dynamics of complex biological systems [45][46][47][48][49][50][51][52][53].…”

“…In this work, we propose a flow of statistical model checking for genetic circuits using Uppaal [41] and D-VASim [39]. In particular, we performed experimentations on genetic circuit models and explored their design parameter sensitivity using Uppaal SMC [42].…”

“…There are a certain number of tasks which cannot be performed in Uppaal [41]. We therefore used D-VASim [39] to address those, which will be detailed in the experimentation section. The paper is organized as follows; Section 2 describes the digital abstraction and a brief introduction to D-VASim and Uppaal SMC.…”

“…As Uppaal does not have the capability to automatically detect the input combination which triggers the output of the circuit, the threshold value analysis of a genetic circuit cannot be performed automatically in Uppaal. D-VASim [39] is the only tool which allow users to perform threshold value and propagation delay analysis of genetic circuits through an automated process [40]. However, D-VASim is not capable of performing the automated statistical model checking.…”