What is Genochemy?

Genochemy is a web application that enables everyone to experience genetic design and synthetic biology through programming a virtual microorganism called "Genomy". While employing an intuitive UI as a visual programming tool, it has the same level of differential equation simulation as modeling in genetic design.

You can play Genochemy here.

Genochemy Basics

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What will Genochemy realize?

Genochemy is a software that will revolutionize educational activities and human practices of iGEM members. Many of the attendees at our educational activities and human practices were not familiar with synthetic biology, so it was sometimes difficult to convey to them correctly and swiftly the design of genetic circuits and how they work. This problem can be tackled with our Genochemy. Its simple and detailed UI is suitable for explaining iGEM activities even to beginners of synthetic biology. Thus, this software will surely help iGEM members to enlighten more citizens about synthetic biology.

It is also useful for the general public to learn about synthetic biology on a personal basis. Not only will it lower the hurdle for many people to start learning synthetic biology, but for those with a special interest in biology or circuit design, experiencing the interdisciplinary world of synthetic biology through actually designing a specific gene will provide a new perspective and explode their interest in synthetic biology.

For educational use, see our Education & Communication page or Details of Education page.

How to use Genochemy

What are on the playfields

Genochemy's screen can be divided into four main areas. (The top right and bottom right can be hidden or pulled out using the "Hide/Show" buttons for those who want to make the most of the screen's width.) Let's first look at what you can do in each of these four places.

Bottom left: Sequence tray

Found here are several types of blocks that play important roles in genes, such as promoters, protein coding regions, and terminators. Each block represents a nucleotide sequence and has a long shape, and you can distinguish which role it plays on the designed gene by its shape. Promoter blocks are the blocks with arrows in blue. The protein coding region block is simply an elongated shape, and the terminator block is red with a T-shaped attachment. Each block has several detailed functions, and from the drop-down box on blocks, you can choose the function that matches the behavior you want to achieve. For example, you can choose the activator’s function from the one that responds to blue light (works like EL222) or that responds to red light (works like PhyB and PIF3). This makes gene design in Genochemy very simple yet flexible, allowing for a very rich design depending on your creativity.

Top Left: Program (Gene Design Place)

Here is where you drag blocks from the Sequence tray and connect them together to make genes. When the "Run = start experiment" is performed, considering a sequence of promoter + protein coding region + terminator as an effective gene, transcription and translation are performed on a simulator running behind Genochemy to calculate how the amount of mRNA and protein actually changes.

Upper right: Laboratory

Here you will find the environmental control panel and Genomy. Genomy is a Genochemy-original microorganism that mimics a real microorganism; when a fluorescent protein is expressed inside Genomy, Genomy changes to the corresponding color to tell you what happened. The environmental control panel allows you to control the dose of drug A and whether illuminating with blue or red light. These represent the environmental factors surrounding Genomy. Moving the slider adjusts the amount of drug given to Genomy, and checking the checkboxes causes Genomy to be illuminated with blue or red light. For example, unchecking the blue light checkbox during execution means that blue light irradiation has been stopped in the laboratory, and the corresponding activation will be terminated.

Here is the section containing a variety of functions, consisting of five tabs (Tutorial, Protein, RNA, Questions, and Load) and a Run button (and a Re-Run button). The Run (and Re-Run) button allows you to run simulations, and the Tutorial, Protain, RNA, Questions, and Load tabs provide information about the experiments you have programmed and general tips for using Genochemy. The Tutorial tab provides well-designed slides and brief explanations to help you quickly learn how to use Genochemy and get started with your design. The Protein and RNA tabs provide a list of validated proteins and mRNAs that are actually produced by transcription and translation in Laboratory, respectively. Clicking on a substance in the list will display detailed information about its function and the mRNA from which it was translated, or the promoter from which it was transcribed, in the case of mRNA. For fluorescent proteins among the Proteins, the actual production rate is shown in a graph plotted based on differential equations. In the Questions tab, there are educational questions with illustrations, and you will be asked to think about the design of the gene that reproduces the function illustrated. For some of the questions, clicking the "Show Answer" button will display the gene sequence in the gene design field as an example of the answer. You can edit and "run" this gene sequence just as you did with your own sequence. The questions here increase in difficulty step by step, so you can deepen your understanding of gene circuit design just by working on these questions. Finally, the Load tab allows you to view the actual sequences used in iGEM UTokyo's Project.

The flow of operating Genochemy

Now that we have explained the playfields, let's look at the actual process of designing and simulating a genetic circuit using Genochemy.

Step1. Design

First, drag a nucleotide sequence block from the Sequence tray and drop it on the gene design site. The nucleotide sequence will appear in the gene design site and be added to the program. Since the original nucleotide sequence remains in the Sequence tray, you can bring the same type of sequence again and again to the gene design site. When moving the cursor over each part in the nucleotide sequence tray, the description is displayed. Before and after this move, select the type of each block from the select box. Repeat this operation several times, and when you have brought some parts from the nucleotide sequence tray to the gene design area, you can start designing gene circuits. The nucleotide sequence blocks can be connected to each other horizontally in Gene Design Place. When a new block is placed close to a block already in the field, the blocks are connected. Once connected, a block can be disconnected by double tapping (clicking) on it. To connect them again, move the block again. You can delete blocks or gene sequences in the gene design site by dragging and dropping them back into Sequence tray. If you want to use a new part while assembling, bring it back from Sequence tray. The basic structure of the gene circuit has a promoter and terminator block with a protein coding region in between. Try to create such a structure.

Tips for efficient programming are here.

Tip 1: Multiple genes can be arranged on the program.

Tip 2: It is possible for multiple protein coding regions to share a promoter (i.e., multiple protein coding regions can be sandwiched between a pair of promoters and terminators). Such examples are found in actual prokaryotes.

Here you complete, at a minimum, the main task of programming.

Step2. Environmental settings & Run

Of course you could start transcription and translation here and be done with it, but Genochemy is a much more powerful software; you can change Genomy's environment! There are three external parameters that you can change: the dose of drug A and the ON/OFF of blue and red light respectively. We mentioned that these can be changed with sliders and checkboxes in "Upper right: Laboratory" under "What are on the playfields". These parameters can be changed either before or during the run, and their reflection in the laboratory is immediate. All that remains is to click on the Run button in the center of the right edge of the screen, and the program will start running and in silico transcription and translation will begin.

Step3. Observation

An experiment must include observations. Now that we have designed the gene, initiated transcription, and translation, and regulated the environment, what do we see as a result? Here you can observe the production of fluorescent proteins. If the gene sequence you have added to the program contains fluorescent protein coding regions such as GFP or mCherry, there will be an entry labeled GFP or mCheery in the Protein tab in the lower right field. Clicking on it will display the current production relative to each protein.

The graphing function was developed in collaboration with iGEM Waseda_Tokyo team members.

See Collaborations page.

Step4. Feedback

Based on the observations results, you can adjust the environmental settings or design a new gene circuit. It is one of the main features of Genochemy that you can easily and clearly turn into such a PDCA cycle.