SynBioKit: A platform to create, visualise and validate biological designs

The Synthetic Biology Open Language (SBOL) is a widely used open-source data standard for reproducible and reusable genetic circuit designs. The latest version of this standard, SBOL3, supersedes previous versions. SBOL3 has several new features and allows for capturing a wider range of essential biological design information concisely and more accurately across different design-build-test-learn workflows. It also enables the creation and integration of a network of information using graph-based technologies. However, SBOL3 is incompatible with the previous versions due to the significant changes, and data exchange and the development of software tools are hindered by the lack of necessary infrastructure. There is an urgent need to develop essential enabling technologies to create, validate, analyse, and visualise designs, taking advantage of SBOL3's new and extended features while supporting existing software tools for migration. Synthetic biologists work with software tools for tasks such as design and visualisation. These tools rely on standard libraries to abstract the details of data standards. However, the community has limited resources. Developing SBOL3 libraries for different programming languages, validation approaches, and compliance is not feasible. Migrating existing tools is challenging also due to the lack of libraries, especially when there are existing and large amounts of information. Providing higher-level interfaces for reusability, automation and best practices is crucial. Moreover, as the SBOL data model evolves to accommodate different and additional types of information, new and extensible visualisation strategies and approaches to intuitively represent and capture data are needed. This project aims to provide a much-needed and one-stop synthetic biology infrastructure. A web-based platform called SynBioKit will be established to create, visualise and validate design information using SBOL3. SynBioKit will be designed as a lightweight and easy-to-use application by actively engaging with the stakeholders. Features will also be accessible computationally to facilitate the emergence of other useful tools and workflows. In addition, SynBioKit will include online resources for community engagement and impact-related activities. Currently, there are no tools providing the services offered by the proposed SynBioKit platform. The following objectives are defined. These objectives will be applied to real-world biological use cases working closely with wet-lab biologists. 1- Enhance the reproducibility and reusability of synthetic biology designs by facilitating their creation easily and intuitively. 2- Research and develop innovative visualisation strategies focusing on different aspects of biological designs across multiple scales. 3- Validate biological designs and visualise issues and errors efficiently for compliance. 4- Support the synthetic biology community in the UK and internationally by making SBOL3 accessible to the wider community via an online platform with standalone and web APIs, backward compatibility features, and community resources. Synthetic biology is a priority area for research councils, including BBSRC. BBSRC promotes knowledge exchange through data standards. Data science, computational and transformative technologies and the development of new tools for data-intensive biological tasks are key components for fostering innovation and world-class research for UK Bioscience. SBOL is an essential enabling technology to support data-related activities, and SynBioKit is expected to be a widely used resource by the community to achieve these goals and support the national vision for engineering biology.