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 induced by 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 comprises four main components:

1. Ensuring Constant Promoter Functionality: To evaluate transcriptional intensity, we utilized the RBS Calculator to analyze the gene sequences. Based on the results, we concluded that the constant promoters performed as expected, meeting the desired performance criteria.
2. Characteristics of Logic AND Gate: We conducted mathematical derivations based on our assumptions and built a control system model to simulate and calculate the numerical relationship between GFP output and various input quantities. By clarifying the relationship between input and output, we presented the logic AND gate characteristics using a quantitative model through control theory.
3. Demonstrating CRISPRi Inhibition: Using Benchling, we designed and optimized the sgRNA sequence. We employed ordinary differential equations to mathematically simulate the expression process of dCas9 and sgRNA, successfully confirming its inhibitory effect on GFP productivity with Simulink. In this section, we outlined a series of important assumptions to ensure our model accurately reflects the inhibition effect of CRISPRi.
4. Estimation of Time Consumption by the Boolean Logic Circuit System: We utilized COMSOL to calculate diffusion time and created a 3D model for simulation and visualization purposes. Our findings indicated that the diffusion time is negligible. Furthermore, we estimated that the output process takes approximately 60 seconds. By comparing this with wet lab results, we concluded that the Register & Patch process requires significantly more time. We hope that by studying this further, iGEM participants will discover ways to reduce wasted time in the future, ideally through the development of an approximation algorithm with controlled error levels.

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.