Workshop

Introduction to synthetic biology

Most of the participants are non-biology workers, who had no basic knowledge in synthetic biology. For public education, as also to prepare them for using MagicBlock, we spent 40 minutes to introduce synthetic biology.

The main goal of this introduction is not to bring details about biotechnology, but to familiar people with the logic of building genetic circuits. Similar to the programming in the IT, genetic circuits also need information inputs, processing, and outputs, which correspond to bio-sensors, bio-logic-gates, and reporters respectively.

We gave three examples to illustrate the basic logics, covering the issue of social problem solving, BioArt design and signal processing.

Mine detection (Social issue)

While there are mine fields from World War II piled up over the years, detecting them becomes a tricky problem. The commonly used metal detector, is not only expensive but labor consuming. Thus, dinitrotoluene sensing bacteria were created. Whenever dinitrotoluene, the decomposed product of the TNT, is present, the bacteria will generate GFP (green fluorescent protein) to alert mine searcher. The three basic element in this case is:

input (dinitrotoluene sensor)— processing (direct) — output (GFP)

To demonstrate the concept of logic gate, we made some extension to this example. Logical processing, the application of logic gates, might increase the accuracy of the detection to a large extent. For instance, co-sensing dinitrotoluene and metal by two sensors, using AND gate, can solve the problem of gas (dinitrotoluene) dispersion.

The three basic elements are then:

Input (dinitrotoluene sensor, metal sensor)—processing (AND gate)—output(GFP)

Synthetic Music (BioArt)

The second example is about art and design, which is an iGEM project done by NYU Shanghai. This example helped in keeping the attention of participants with background in designing. They made full use of the randomness of biotics to show the beauty of the nature. They made a device to detect the position of fluorescent light in culture dish and then generate electronic sound. They were able to make a synthetic music eventually.

The three basic elements are:

Input (direct)—processing(oscillator)—output(GFP/RFP/YFP)

Bio-adder (signal processing)

This might be intriguing for experts from the Information Science to design a Bio-adder. In this case, the most complicated part is processing, which includes multiple logic gates like NOR gate, AND gate and OR gate.

The three basic elements are:

Input (fluorescent sensor)—processing (digital circuit of Adder)—Output(GFP)

After these three cases, the participants had a better understanding of the circuit designing logic, and got an overall impression about synthetic biology.

Hardware & Software display

The previous session has prepared the participants with basic knowledge of synthetic biology. There are three main elements in the gene circuit designing session: input, processing, and output.

However, designing genetic circuits has a high bar in expertise, which might be too complicated for non-biology workers. In addition, due to the relatively small gene capacity of a regular plasmid, putting all element gene in one plasmid is very challenging even for experts.

To help makers to realize their enlightening designs, we invented MagicBlock, a set of gene logic gates, including the interactive software and automated hardware, to reduce the bar for constructing genetic circuits. By separating each element into different plasmid and allowing bacteria to pass on signal by the Quorum Sensing system, it not only allows us to acquire the infinite extendibility of gene circuits (at least in theory), but also helps makers to visualize the gene designing process and assist them designing bio-products without doing experiments.

The software was downloaded by each participant, with the assistance of 5 iGEMers. The participants were trained to use it by written guidance. By running one example, we showed participants how software and hardware were integrated.

The participants used their basic computer science knowledge to understand the circuits in the software, while the hardware could show them the synthetic biology version equilibrant to the software circuits.

Fig8.Our team member is assisting makers uploading the software file onto the Robot.







Fig9. Makers are learning to edit their design on the software. In this case, the maker called Froffy was trying to make a heat-controlled bacteria panel.







Fig10. In order to find fluorescent reporters, Froffy searched on the software.

Design Thinking Class with genetic circuits

Design thinking is a method for practical, creative resolution of problems. It is a form of solution-based thinking with the intent of producing a constructive future result.

[ Dorst, Kees; Cross, Nigel (2001)."Creativity in the design process: Co-evolution of problem-solution". Design Studies. 22 (5): 425–437.]

Here we introduced the complete process of design thinking, including proposing ‘How might we’ (HMW) questions, researching, revising HMW questions, and producing solutions.

We told participants that they needed to tell others a story, whether it was a social issue or BioArt. Since time was limited, we encouraged telling bold hypothesis rather than detailed research.

For the solution part, each group were required to design a synbio-product based on the HMW question they’ve raised. To visualize their design, we brought a set of stickers with us.

Fig11. Red stickers represent inputs, including example sensors like heavy metal sensor and light sensor; yellow stickers represent logic gates, enabled participant to structure gene logic; blue stickers, likewise, represent outputs. Some blank input and output are made for the purpose of inspiring participants’ imagination. Fig12. The participants used the stickers for brainstorming and illustration, software and robot for debugging.

While using stickers to brainstorm and illustrate their design, they were making full use of MagicBlock software and hardware. Dragging elements they’ve designed by stickers into the software could assist them to debug. After uploading their file onto the hardware, they could see how signal was produced by bacteria (represented by red ink due to the biosafety regulation) diffuse in the culture.

One hour’s discussion has generated excellent designs.