Gene-circuit, as a software, adopts an intuitive UI for visualization programming, the main purpose is to allow users to build. Complete genes with different functions through multiple combinations of the 12 synthetic biology components given by the software, to realize the precise regulation of glucose concentration and fluorescence, to deepen the understanding of the whole project, and also to help users to experience the design of gene components in the process of splicing again.

Click on the link here to download and learn more about Gene circuit

In any case, we expect that Gene-circuit can be a software that helps the overall project understanding and knowledge learning related to synthetic biology. As mentioned above, through the intuitive UI for visual programming, Gene-circuit allows people who are relatively unfamiliar with the background knowledge of synthetic biology to quickly and accurately understand the. overall principles and content of the project, and to successfully stitch together a reasonable combination of genes to dynamically regulate glucose concentration. in a visual form, with as little need for basic knowledge as possible. Enhance the overall understanding of the project.

We have made a lot of efforts to realize the non-specialization of the software. Firstly, the core module of the whole software adopts a jigsaw-like gameplay, which breaks down the complex eukaryotic gene structure into concise and intuitive gene components ,and simulates the complex process of building synthetic biology target genes through simple splicing of the gene software; secondly, there is an all-around detailed tutorial of splicing in the lower-right part of the software, which vividly displays the component combinations that should be constructed under various circumstances in the tutorial area in the form of illustrations and result images.  

Secondly, the lower right part of the software has a comprehensive and detailed splicing tutorial, which vividly displays the combinations of components that should be constructed under various circumstances in the form of illustrations and result images in the tutorial area, and also sets up a one-button construction structure to meet the needs of rapid understanding of the project.  

Finally, the software also links the micro-level gene construction with the macro-level blood glucose regulation and fluorescence intensity, especially in the aspect of blood glucose level regulation, the software has reproduced the results of the project's mathematical modeling of blood glucose concentration and insulin concentration as completely as possible, and finally displayed them in the form of an easy-to-accept visual function image in the upper right part of the software, so that every time a qualified gene is constructed, the function image in the upper right corner will be displayed as a function image. Whenever an eligible gene is constructed, the function image in the upper right corner can give the corresponding changes in a macroscopic perspective, so that the user can understand the central role of each component in blood glucose regulation.  

In summary, Gene-circuit, through its highly open rules and combinatorial approach, and its visual presentation of different scenarios, is dedicated to providing synthetic biology professionals and enthusiasts interested in the project with an in-depth understanding of the combinatorial rules and fundamentals of synthetic biology, as well as a deeper understanding of the full project.

the main body of Gene-circuit consists of two main areas: the interaction module on the left side and the result presentation module on the right side; the interaction module is divided into the original area on the lower left and the combination area on the upper left, and the result presentation module is divided into the tutorial area on the lower left and the result area on the upper left.

The element area is used to store unassembled gene elements and consists of promoter elements and coding region elements. Wherein the promoter elements are shown in the form of elements with an arrowhead shape. The coding region elements are displayed as relatively elongated elements. Based on the basic principle of eukaryotic gene composition, the promoter element should be at the forefront of the gene, and the promoter tail connects to the corresponding coding region element, which finally constitutes the mature eukaryotic gene sequence.

In the assembly area, you can assemble components to create genetic circuits. The components of the genetic circuit come from the promoter block prevented at the beginning of the component area and the protein coding region. It should be noted that since the sequences of the non-coding regions at the 3' end are roughly the same, we have not represented the 3'UTR part as a separate element in this software for the sake of simplicity and have uniformly omitted this part, so that you do not have to take the specificity of this part of the sequence into account fully when splicing.

The "Tutorials" section consists of three columns: "Tutorials"," Questions" and "Loading". The "Tutorial" option allows the user to learn about Gene-circuit tutorials, where most of the questions you may have during the splicing process can be answered, and the accompanying images will deepen your understanding of the tutorials, or you can save time by selecting the Load option in the tutorials for one-click splicing. The "Questions" option provides several genetic circuit quizzes with answers. This will help you deepen your understanding of the whole project and synthetic biology. From the "Load" tab, you can load a sequence that simulates the iGEM project. 

In the Interaction module, you can build a specific gene by combining gene elements organically: first, drag and drop gene elements from the element area to the combination area. You can combine two originals by placing the element dragged by the mouse close to an existing element in the Combination area. To separate a specific element from other elements in the program, double-click on it. Blocks that are no longer needed can be dragged and dropped in the component area. In the Results Presentation module, you can adjust two parameters separately: the initial blood glucose concentration and the presence or absence of blue light exposure to change the environmental variables.

After adjusting the simulated environmental conditions, you can press the evaluate button and the program will give you the corresponding blood glucose concentration, insulin concentration and fluorescence intensity in the upper right results area, based on the results of your splicing in the combination area.

The observation of green light and blood glucose concentration allows you to evaluate the effectiveness of the build. On the one hand, you can modulate the initial simulated environmental conditions in the resultant area in real time and observe the dynamics of the results, and you can also consider improvements at the level of the genetic components for the next step of the build.

The core function of this software, i.e. gene component splicing, is not set as a standard answer, all original splicing combinations in line with the eukaryotic gene expression paradigm are permitted, and a series of fluorescence, blood glucose, and other information corresponding to the corresponding component combinations will be displayed in the result area, which maximally retains a high degree of freedom of the component splicing process to ensure that you can effectively simulate the process of blood glucose regulation in different situations on this software. The software can effectively simulate the process of blood glucose regulation in different situations. This will help you to understand the specific role of each gene element in the project from a macroscopic point of view.

As long as there are no errors of principle in the splicing of the components, the corresponding blood glucose concentration will be given as a dynamic function graph in the results area in real time. According to the corresponding blood glucose trend, you can make timely adjustments to the splicing results of the gene software, and along with your adjustments, the blood glucose concentration will instantly change accordingly. The construction of this "gene-glucose" purpose-oriented real-time adjustment system aims to minimize the amount of unnecessary thinking, enhance the intuition of the software, and help you to produce a relatively tangible and perceptual knowledge of the whole process of blood glucose adjustment.

2024 Competition / Software Tools / CSU-CHINA · GitLab (igem.org)

This project has been open sourced on this website, if you are interested, you can get the original code of the project at the above URL.