Overview

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

Thus far, a lack of methods for efficient and proof-of-principle design may limit their wide acceptance in synthetic biology. For instance, CAST (developed by our team SYSU-Software in 2013) is a software for convenient de novo circuit design^[2]. However, on one hand, for a beginner, a dearth of frameworks for the reliable construction of complex, higher-order systems^[3] makes arrangement of parts into circuit topologies somewhat 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 deduced 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 an 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 rader 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] makes possible the framework-based construction.

Characterization and Standardization of a Circuit or System -- Our Goal

So far, a considerable number of synthetic biological parts and devices have been characterized and standardized^[4], but not circuits nor systems. Although we could theoretically ensure a functional system based on frameworks, we could not determine the actual performance of a system through the parameters of its parts. Furthermore, standardization is useful in creating circuits or systems that can be used in a plug-and-play fashion to construct larger networks^[4], but there are still not enough standardized circuits or systems. Cameron et al.^[5] pointed out that in the near future, workflow for a biological circuit engineer will be limited by their capability of analyzing circuit behaviors and incorporating the data into the next design cycle.

To tackle these problems, we can learn from the mature methods with which synthetic biologists or iGEMers can characterize and standardize a biobrick. We propose that we could characterize and standardize a circuit or 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 circuit or system. And the Vector sub-module in FLAME may be helpful in standardization of a circuit.

Improved Simulation and Experiment Modules -- Improvements as well as Innovations

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 make sure that they simulate the experimental results more efficiently. For the Experiment module, experimental protocols for ordinary used are provided as reference.

We also developed an online blast software, Biobrick Blast Online (or BBO for short), as our Human Practice project, to aid in 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!

[1] Sprinzak, D. & Elowitz, M.B. Reconstruction of genetic circuits. Nature 438, 443-448 (2005).

[2] https://2013.igem.org/Team:SYSU-Software

[3] Lu, T.K., Khalil, A.S. & Collins, J.J. Next-generation synthetic gene networks. Nat Biotechnol 27, 1139-1150 (2009).

[4] Canton, B., Labno, A. & Endy, D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26, 787-793 (2008).

[5] Cameron, D.E., Bashor, C.J. & Collins, J.J. A brief history of synthetic biology. Nature reviews. Microbiology 12, 381-390 (2014).