Overview

One method frequently adopted by synthetic biologists is the reconstructive approach; that is, by designing and building genetic circuits with similar functions, synthetic biologists can gain insight into the underlying mechanisms of the naturally occurring circuits.[1] Many software aiming at facilitate the in silico design of genetic circuits have been developed.

Thus far, a lack of methods for efficient and proof-of-principle design has limited their wide acceptance in synthetic biology. For instance, CAST (developed by our team SYSU-Software in 2013) is a software for more convenient de novo circuit design, but on one hand, for a beginner, a dearth of frameworks for the reliable construction of complex, higher-order systems[2:Next-generation...] makes arrangement of parts into circuit topologies annoying and frustrating, let alone construction of a FUNCTIONAL circuits only by linking the scattered biobricks together in CAST. On the other hand, the performance of a system cannot be determined through individual parts. An expert synthetic biologist may want not only to build a functional genetic circuit, but also to characterize its performance.

So a software endowed with the capacity of more efficient and reliable design is needed. Based on the idea of framework, our latest software FLAME, short for Framework-based Layout And Metacircuit Design Engine, is a tentative exploration of solutions to the problems mentioned above. Features of FLAME are as follows.

Framework-based Circuit Design -- Core of FLAME

Framework-based method is the core of FLAME to ensure the EFFICIENT construction of a FUNCTIONAL circuit. After users select the input, output and the topologies (provided as “frameworks”) of the system, several solutions are provided when you choose your ideal framework., each of which differs in mechanisms and efficiency (for example, genetic AND GATES can be achieved by protein-protein interactions or substrate-receptor interactions; they are different in many aspects). According to the performance of each solution (shown in the form of radar charts), users can select one and fine tune the details of the circuits. The fact that most synthetic circuits are still made up of a limited but sufficient number of commonly used components (such as LacI, TetR and lambda repressor proteins and regulated promoters) [3: next...] makes designing genetic circuits based on functional frameworks possible.

Characterization and Standardization of a System

Although we could ensure a functional system through designs based on frameworks, it would be important to characterize systems simply because we could not determine the actual performance of a system through the parameters of its parts. To try to tackle this problem, we can learn from the mature methods synthetic biologists and iGEMers use to characterize and standardize a biobrick. We proposed that we can characterize and standardize a system in a similar way, though with more inputs and outputs. FLAME provides simulations on Dynamic Performance, Static Performance and Expression Efficiency, all of them providing important clues on the performance of the designed system.

Refined Simulation and Experiment Modules

Simulation and Experiment modules are important components of both CAST and FLAME, and we update them so as to work with balance between efficiency and accuracy. We rewrote our algorithms to ensure that they simulate the experimental results with more efficiency. For the Experiment module, we give up the tedious experimental protocols ways, but provide experimenters with chance to record their procedures and warnings of experiments on the software, and to share them with other software users.

We also developed an online blast software, Biobrick Blast Online (or BBO for short) , as our Human Practice project, to aid the recognition of a possible biobrick from a DNA sequence. We believe that with FLAME and BBO, users can be more confident in their efficient constructions of reliable genetic circuits!