Engineering your cells with sequential logic can give them incredible capabilities. However, it requires great effort to proceed from functional specifications to real plasmid vectors. Carpiod is a tool meant to ease the procedure. We developed a user-friendly, open-source tool, Carpiod. Carpiod is a program that allows users to define a sequential sequence function. It then generates plasmids containing fully functional circuits. First, we built a user interface to specify circuit function, which is very easy to understand and use. Then, we used experimental data and modelling methods to evaluate the performance of candidate circuits and select the best solution. Furthermore, we created a database, including all the parameters of available recombinases and other basic parts. After the 2017 iGEM Giant Jamboree, we plan to continue working on the database to make it fully available for all users to access and contribute.

During the preparations for iGEM 2017, we developed a tool intended to help users design sequential biological circuits for their customized objectives. After the user defines a series of sequential functions for the cell, the program returns one or more possible plasmid designs that, once put into a host cell, will execute the function exactly as the user defined. This circuit can direct the cell to perform a series of functions in specific order. Some synthetic biology software applications require users to express designs in a newly defined language. We think it is necessary to reduce the learning effort required by the tool. In electronics, engineers use a hardware description language to design circuit functions. Although not difficult, learning any programming language can be challenging for beginners. Therefore, we wanted to open up RASSD to people who had no previous programming experience, thus eliminating the initial learning curve normally imposed by this technological barrier. Consequently, we developed an intuitive drag-and-drop user interface.

Graphical User Interface

Some synthetic biology software applications require users to express designs in a newly defined language. We think it is necessary to reduce the learning effort required by the tool. In electronics, engineers use a hardware description language to design circuit functions. Although not difficult, learning any programming language can be challenging for beginners. Therefore, we wanted to open up RASSD to people who had no previous programming experience, thus eliminating the initial learning curve normally imposed by this technological barrier. Consequently, we developed an intuitive drag-and-drop user interface.

Model

State transitions in our design are implemented by bio-flip-flops. To prove that the circuits of our design can meet customer needs, we performed a simulation of a complete bio-flip-flop state transition cycle. The parameters of integrases and their corresponding excisionases were estimated from the results of characterization experiments.

Furthermore, there are also extensive model-experiment interactions in the scoring and screening process of candidate circuits. First, our scoring criteria favor fewer parts and terminator inversions. This is backed by evidence from experimental observations. Moreover, the performance of the design can be simulated on a population level, and optimized induction time separation can be determined.

Database

The bio-flip-flops in our design only use three well-characterized integrases: Bxb1, TP901-1 and PhiC31. Previous work has reported a set of more than 10 orthogonal recombinase genetic parts. Clearly, the number of available recombinase parts will expand, and our knowledge of them will deepen. We expect to develop a database of recombinase part characteristics, so that users can get access to their dynamic properties and experimental data. Contributions are also welcome.

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