Our iGEM Groningen 2023 team has made substantial contributions that will have a lasting impact on future iGEM teams. These contributions encompass a range of areas, including Software and Hardware, Human Practices, and Engineered components. We believe it is important to establish meaningful contributions, as this underscores the core principles of scientific progress.

Throughout the iGEM competition, teams are charged with the safe implementation of their projects, the development of innovative strategies, and the creation of novel genetic components. In our view, the essence of science lies in building upon the knowledge of those who came before us, with the aim of achieving higher goals. The contributions made by each iGEM team lead to the recognition of more intricate challenges, as previous issues have already been resolved. This continuous cycle of improvement propels the advancement of scientific understanding and fosters innovation.

Our team successfully designed a cheap, easy to build and use, modular biosensor that is able to sense not only LED lights but also fluorescent proteins such as GFP. We outline the development of a potentially inexpensive, readily manufacturable, and modular sensor for biofilm detection, particularly on medical implants. The impact is significant as it could enhance medical implant monitoring and infection control.Future iGEM teams can benefit from this by utilizing the provided design, material list, instructions, and Arduino code to build their own biosensors.

The modular nature of the biosensor allows for customization, making it adaptable to various needs. Future iGEM teams can find a detailed set of instructions and detailed information, including experimental methods, hardware setup, and considerations in the provided text, with specific sections and diagrams outlining the components and processes involved in the biosensor development. iGEM teams will be able to build this sensor for themselves and adjust it to their specific project needs. For more information, visit our Electronics page.

In addition to the biosensor, our repository includes comprehensive instructions for teams interested in creating their own biosensing applications. This package encompasses an Arduino-based sensor code for real-time data acquisition, integrates with the Google Cloud Platform (GCP) backend for efficient data management, and offers user-friendly mobile and web applications for real-time data visualization and interaction. This information plays a pivotal role in advancing the field of healthcare by delineating the software architecture and design essential for the detection and treatment of biofilm infections. Its significance lies in the capacity to enable early detection, real-time data visualization, and user-friendly interfaces, ultimately enhancing patient outcomes and healthcare management.

For the benefit of future iGEM teams, we have made our entire codebase accessible via our repository, fostering collaboration and innovation within the iGEM community. Moreover, our detailed documentation of the software architecture, design principles, and development process serves as a valuable resource. You can find in-depth information on these aspects, along with references to our web application and GitLab repository for further exploration and collaborative efforts on our Software page.

We have designed and detailed the PHAGER-M13, a modular and visually appealing hardware device for the Bye-O-Film project. This device seamlessly bridges the realms of health and aesthetics, offering a spectrum of choices in materials, colorways, and user comfort. Our documentation serves as a vital resource, shedding light on our meticulous design process, encompassing aspects like user comfort, material selection, aesthetics, and scalability. It underscores the significance of blending functionality with aesthetics in the realm of healthcare devices.

For the benefit of future iGEM teams, we have compiled a comprehensive account of our product design journey. This includes our research, ideation, prototyping, digital design, user-centered approach, sustainability considerations, and adherence to regulatory standards. This holistic documentation serves as a valuable reference point for teams embarking on their hardware prototype development journey with a strong emphasis on design and user experience. For detailed insights into the PHAGER-M13 design process and considerations, please refer to the provided text on our Product Design page.

We contribute to the iGEM community by providing a diverse range of biological parts, including mainly composite components. A basic part is the codon optimized coding sequence of FleQ BBa_K4720000. Composite parts, labeled BBa_K4720011 to BBa_K4720021, are also provided. Additionally, we have designed new parts (BBa_K4720101 to BBa_K4720105), which are planned to be made in the future. These include coding sequences and genetic cassettes. The contribution of these parts to the iGEM Registry helps expand the available genetic building blocks for synthetic biology projects, fostering collaboration and innovation within the iGEM community. This contribution aligns with the "Get and Give" philosophy of iGEM, where teams both receive existing biological parts and contribute new ones to the Registry.

One of our notable contributions is BBa_K4720021, a well-documented biosensor part with a focus on modularity, versatility, and functionality. This genetic component holds immense value for biosensor development, particularly in the context of detecting biofilm formation on medical implants. Future iGEM teams can leverage our comprehensive documentation, design insights, cloning strategies, and assembly solutions, saving valuable time and effort. Future iGEM teams can benefit from iGEM Groningen's work by accessing comprehensive documentation, design rationales, cloning strategies, and assembly challenges related to BBa_K4720021. This information facilitates the incorporation of the part into their projects, saving time and effort. For detailed information about BBa_K4720021, including its design improvements, cloning strategies, and primer sequences, you can refer to the Engineering and Parts page.

In our journey to develop a comprehensive survey for our project, our team drew inspiration and valuable insights from our predecessors, iGEM Team Groningen 2022. While we retained and integrated many of their recommendations, we also expanded upon their guidance, adapting it to our unique project needs. Our aim was not only to build upon their foundation but also to contribute fresh perspectives to the evolving landscape of responsible survey design within the scientific community. We made contributions to the iGEM community's understanding of effective survey design through several innovative additions and expansions. 

We prioritized enhancing survey comprehensibility by incorporating elements such as eye-catching visuals, clear section divisions, comprehensive introductions, progress bars, and estimated time consumption. These enhancements aimed to encourage participants to complete the survey in its entirety, recognizing the impact of aesthetic features on responses and outreach. Additionally, we leveraged Google Forms' advanced features to streamline the survey experience, directing participants to relevant sections based on their responses. We further improved the informed consent form's clarity by organizing information under question subtitles, facilitating a more comprehensive and enjoyable participant experience.

In an effort to obtain more personalized end-user insights, our team adopted an organic approach by designing posters with survey links in both English and Dutch. While our initial plan involved displaying these posters in medical facilities with stakeholder support, we also recognized the importance of visual design in reaching our target audience effectively. In addition, our team faced challenges during the ethical review process and hospital survey placement, highlighting the importance of early ethical review initiation. To overcome these setbacks, we exhibited flexibility by placing posters in physiotherapy practitioner offices, university bulletin boards, city bulletin boards, and sharing survey links online. This adaptability demonstrated our resourcefulness in survey dissemination, ensuring continued data collection despite obstacles.

These novel elements introduced by our team, including improved comprehensibility, an organic approach to engagement, and flexible distribution methods, significantly enriched our survey development process. While building upon the foundation laid by the 2022 team, these additions enhanced the effectiveness, inclusivity, and resilience of our survey. Our aim was to contribute to the evolving landscape of responsible survey design within the scientific community, providing transparency and inspiring future iGEM teams to consider not only survey content but also supplementary materials in their survey execution and distribution. Detailed information on these contributions can be found on our Surveys page, under the "New Additions and Expansions by iGEM Team Groningen 2023" and "Questions & Poster" sections, which provide valuable insights for other teams seeking inspiration and guidance in their survey endeavors.

Complementary to expanding the information on how to conduct a good survey, we included transparent information on how to make an interview outline and we shared instructions for the interviewer. In addition, the interview directions reflect the information from our survey, illustrating for other iGEM teams how they can incorporate and reformat questions used for a survey into interview questions. More information about this is available on the Surveys page under the Interview section.

Although our project is based on proof of concept, and application outside of the lab is not within the scope of this specific project, we nonetheless have contributed a basis of knowledge for other people to build on. An overview of all future prospects considerations can be found on the Future Prosepcts page.

Biology:
Design: We have designed many (modular) plasmids that can be cloned and adjusted, with scientific literature to support our design decisions. New iGEM teams can take the research we did and expand on it, bringing the idea closer to real-world applications. Results: We tested several of our designed constructs, and the results we generated can be used by other iGEM teams to build upon. Through our experiments we found what works and what doesn't in terms of design and cloning strategies. This paves the way for other teams to conduct follow-up studies, contributing to the expansion of the knowledge base. Future: We hope future iGEM teams can take the knowledge we generated and build upon it. Both our biosensor component and our phage display design are thoroughly discussed on the wiki and the improved design of the cyclic-di-GMP promoter is added to the Parts registry.

Hardware:
We designed, built and tested a sensor which is able to sense fluorescent proteins. Future steps would include dual sensing both the RFP and the GFP and creating a sensor + program system that can differentiate between the two. We also discussed using filters to prevent the excitation light from activating the sensor in a real-world system. Additionally, this sensor could be adjusted to have a higher sensitivity in order to detect lower concentrations of fluorescent protein.

Software:
Design: We created an app that can showcase real-time data along with health related information and contact information of healthcare providers. Future teams can use our code, considerations and setup instructions to create their own app and to build on the design. More information can be found on the Software page.

Bringing it all together:
What would our device look like if it were made? This was a question we asked ourselves and set out to answer. We bought each of the components together to produce a conceptual design. This includes the entire system from infection to notification, as well as 3D blueprints for the device itself. For more information, please see our Project Description and Hardware pages.

Figure 1: Schematic overview of the design implementation - created using BioRender.com.

Figure 2: Internal design of the PHAGER-M13.

Within our project, we've embarked on creating a modular biosensor with a current focus on biofilm treatment. This biosensor boasts three interchangeable modules: the sensor module, the reporter module, and the effector module. To underline the versatility of our design, we've also put forth an alternative theoretical luciferase-based reporter module. This forward-thinking approach ensures that upcoming teams will have the flexibility to select one or multiple modules, providing them with a robust foundation to construct their own biosensors, complete with effector functions.

Our commitment to sharing knowledge extends to our comprehensive detailing of cloning strategies for specific components. Throughout our project, we've expertly employed three distinct cloning methods: conventional, Gibson assembly, and Golden Gate. This information holds immense significance as it offers invaluable insights into the cloning strategies and design decisions that shaped our project. By openly sharing our experiences and strategies, we aim to assist future iGEM teams in comprehending the intricacies and considerations inherent in the development of similar genetic constructs geared towards biofilm detection and treatment.

The impact of our contribution extends beyond the iGEM community, benefiting the broader field of synthetic biology. Future iGEM teams stand to gain substantial advantages from our meticulously documented journey, thereby enhancing their ability to navigate similar challenges and pitfalls in their own projects. These insights cover various aspects, ranging from the intricacies of reporter and sensor module design to effectively managing recombination issues and harnessing the potential of phagemids for targeted biofilm treatment.

Within our project, we've provided a comprehensive account of the troubleshooting process undertaken during the testing phase, focusing on the intricacies of addressing issues related to the functioning of FleQ and the response to cyclic-di-GMP. The significance of this documentation lies in its ability to showcase our team's unwavering dedication to ensuring the reliability and accuracy of our biosensor, an essential component for the overall success of our project. It highlights the importance of thorough problem-solving and serves as a guide for future iGEM teams grappling with similar troubleshooting challenges.

Future iGEM teams can derive substantial benefits from this wealth of information. By delving into the systematic approach employed by our team, they can gain insights into the practical application of techniques such as PCR, sequencing, transformations, and repeated experiments. Armed with this knowledge, they will be better equipped to tackle their own project challenges, ultimately promoting precision and functionality in their synthetic biology endeavors. For those seeking a more detailed exploration of our troubleshooting journey, our team's Notebook and Experiments pages offer a wealth of comprehensive documentation. These pages likely contain a treasure trove of information related to the encountered issues, the methods meticulously employed for resolution, and the outcomes of these concerted efforts.

Our commitment to aiding future iGEM teams extends to comprehensive documentation, ensuring accessibility and ease of use. We have provided essential information such as primers designed for constructs and clear, user-friendly instructions for creating a light sensor and an application. The emphasis on ease of use and modularity amplifies the advantages of our contributions, making them particularly accessible and advantageous.

The code for the Arduino and the code for the Bye-O-Film software can be accessed through our iGEM GitLab repository. This approach significantly streamlines the path for future teams, sparing them from the need to reinvent the wheel. Instead, they can direct their efforts towards building upon the solid foundation that has been laid. Our hope is that this approach will not only assist future teams but also contribute to the vast knowledge base that the iGEM community has meticulously amassed over the years.

Furthermore, we've left no stone unturned in documenting essential aspects of our project. From cloning strategies to tips and instructions on using the provided parts, our comprehensive documentation is a valuable resource for future iGEM teams. During our project we especially encountered the lack of transparency regarding sequences. Therefore we presented our gene map files. All in all we ensured that future iGEM teams have the necessary tools and guidance at their disposal for success in their synthetic biology endeavors.

Within our project, we've embarked on creating a modular biosensor with a current focus on biofilm treatment. This biosensor boasts three

We have shared the things we have learned from designing an electronic sensor for measuring light in the iGEM Collaborative Biosensor Manual. This manual is an initiative of Edinburgh's iGEM team to help current and future iGEM teams working on biosensors. The manual can be found here.