Wet Experiment
Safety
Conducting experiments with viruses safely is a challenging task. For our proof-of-concept, we carried out experiments using influenza virus, but it was difficult to design a safe experimental plan. One reason was that very few iGEM teams had previously handled viruses, and thus it was unclear what information should be included in the Safety Form and the experimental plan.
Therefore, we compiled the key points that iGEM teams working with viruses must investigate and incorporate into their experimental planning. Throughout the text, we use our influenza infection experiments this year as a concrete example. This compilation is based on advice we received from the iGEM Safety Committee and experts in viral infection experiments, highlighting the issues that must be considered from both safety and legal perspectives.
By reading our Safety Document, future iGEM teams will gain a clear understanding of the critical points they need to keep in mind in order to conduct viral infection experiments safely. In this way, our work contributes to improving biosafety within the iGEM community and encourages more teams to pursue ambitious, virus-related projects.
For further details, please see our Safety Page.
Dry Experiment
1. Infection Dynamics Modeling
We developed a minimal mathematical model to evaluate how apoptosis intensity affects the basic reproduction number (R₀) of RNA viruses at the cellular infection level.
To improve the validity of our mathematical modeling:
We minimized the model structure to enable rigorous mathematical derivation and clear understanding of threshold dynamics.
We implemented a stepwise parameter estimation method across multiple experimental datasets, improving inference reliability and reproducibility for wet-lab–based modeling.
- Future teams can use our approach to create more persuasive infection models, especially for evaluating antiviral mechanisms at the cellular level.
2. Protein Design Workflow: EVOLVE
During optimization of RIG-I-based sensors, we faced the challenge of introducing mutations that preserve structural integrity while enhancing target recognition. To solve this, we developed EVOLVE, a Python-based computational workflow for rational protein design.
Key features:
- Accepts multiple interaction conditions
- Provides customizable mutation suggestions
- Simple input/output formats
- Includes a detailed user manual for immediate use
EVOLVE is especially useful for teams designing biosensors, fusion proteins, or immune effectors. It streamlines the in silico design process and complements wet-lab protein engineering.
- For detailed protocols and data, please see our Model Page.
Fig2. Conceptual Diagram of EVOLVE
Integrated Human Practices
In recent years, iGEM has placed strong emphasis on interviewing a wide range of stakeholders. However, we believe that simply increasing the number of interviews can risk lowering the overall quality of Human Practice (HP). In fact, we have observed past cases where HP interviews included questions that could have been answered without conducting an interview at all. Based on this, we concluded that effective HP requires prioritizing stakeholders according to the project’s stage of development, and we developed a methodology called the Compass Tree.
In the Compass Tree approach, the team adapts its choice of interviewees depending on the phase of project development, prioritizing those whose input directly influences decision-making. Before each interview, the team organizes possible options internally and selects stakeholders who can provide perspectives relevant to those options. This ensures that every interview directly contributes to project improvement, rather than becoming a mere “numbers game.” At the same time, we recognized that interviews without predefined options can also be valuable, and we incorporated these strategically into the later stages of the process.
By using Compass Tree to refine their stakeholder mapping, iGEM teams can reduce the burden on all parties involved and carry out more efficient and impactful Human Practice. Future iGEM teams should focus on stakeholder engagement that is tightly linked to decision-making, thereby raising the quality of their HP activities.
Just as travelers need a compass to walk in the right direction without losing their way, iGEM teams need a guide to navigate HP effectively. We hope that our proposed Compass Tree will help future teams conduct meaningful Human Practice. At the same time, we look forward to seeing the iGEM community continue to improve and refine Compass Tree in the years to come.
For further details, please see our Integrated Human Practices page.
Fig3. Logo Image of Compass Tree