This year, we are implementing a cross-disciplinary project, mixing the knowledge from different fields to coordinate them. Since we are constructing a compatible platform this year, we have designed and created modules, from wet-lab to dry-lab, which could be useful for future iGEM teams. In the process, we have met several problems and gained valuable experiences dealing with them. We have built general and delicate models, software, and parts. Here is a short summary of our contribution:

Model: predictions of productivity and efficiency, evidence of inhibition of CRISPRi, estimation of time Software: an NLP-based search tool for iGEM standard parts, Ask Lantern. Parts: part collection including a series of serine integrases and their specific recognition sites, constitutive and inducible promoters, and so on.

Model

Our model consists of three parts.

The first is predictions of productivity and efficiency. On the one hand, we use the RBS-Calculator, a mature software tool, to ensure constant promoter functionality and explore the relationship between the distance from the promoter to the start codon and expression efficiency. This provides iGEM teams with future research ideas for efficiency improvement.

On the other hand, we do mathematical derivation based on our assumptions and build a control system model to simulate and calculate the numerical relationship between GFP output and various input quantities. By building a control system to simulate with Simulink, we successfully verify the function of the logic AND gate and clarify the relationship between Input and Output from a qualitative and quantitative perspective.

The second is evidence of inhibition of CRISPRi. We use ODE to mathematically simulate the expression process of dcas9 and sgRNA and successfully confirm its inhibitory effect on the productivity of GFP with Simulink. Here we state a series of important assumptions to ensure our model can simply and properly reflect the inhibition effect of CRISPRi.

The third is an estimation of time consumed by the Boolean logic circuit system. With Comsol, we calculate the consuming time of molecules crossing cell membranes and build a 3D model for simulation and visualization. We conclude that the time is short enough to be ignored. Moreover, we estimate that the process of Output takes about 60 seconds. So by matching with wet lab, we conclude that the process of Register&Patch takes much time and we hope by studying and exploring iGEMers can find ways in future studies to reduce wasted time if an approximation algorithm with error multiple controlled at a constant level is found.

Software

We have developed a powerful search tool, Ask Lantern, specifically designed for iGEM standard parts. Leveraging advanced models like Llama3 and BERT, we trained Ask Lantern using comprehensive data from parts.igem.org. This tool maps part names to their functional meanings, enabling users to search efficiently using natural language descriptions instead of traditional keywords. Ask Lantern enhances search efficiency, helping users quickly find the optimal BioBrick from the extensive database. Our wetlab team has validated its effectiveness, and we believe it will greatly assist other teams in their BioBrick exploration. We also aim to inspire further innovation in applying large language models in software projects. In addition, we have developed a bioinformatics circuit visualization tool to enhance the application of our project.

Parts

This year, our project includes a series of serine integrases and their specific recognition sites, expanding the basic parts of iGEM. Our composite parts include some inducible promoters, providing more possibilities for gene pathway design. Our parts collection combines many integrase recognition sites, constitutive and inducible promoters, CRISPRi, and quorum sensing elements. These elements interact to form an exquisite, controllable logic system. We verified the control system's feasibility through experiments and Model. We hope these parts can be further explored and improved, contributing to the synthetic biology community.