LIVEBIO: Light-weight Verification for Synthetic Biology

Lead Research Organisation: University of Bradford
Department Name: School of Engineering and Informatics

Abstract

The 21th century will be the age of Biology, tackling global challenges, including -but not limited to- understanding and curing diseases, repairing defective genes, combining natural and synthetic tissues, enhancing crops with biotechnologies, reproducing organs using stem cells, etc. [Chief Scientific Adviser to The President of the EU Commission].

Synthetic Biology (SB), referring to the design and engineering of biological components and systems that do not already exist in the natural world, will play a key role in addressing these challenges by providing a radical step-change in our ability to design and construct multi-scaled biological systems.

Along with the advances in the wet lab and computational methods, the functionality and complexity of SB systems are steadily growing, which brings in a major issue: the likelihood that faults and flaws existent in these systems. This can result in the construction of bio-parts and components that are faulty by design.

At the moment, there are no established methods in SB to find errors and verify correctness. The current practice is limited to understanding the sub-cellular molecular machinery in wet-lab environments, which is costly and extremely slow. The existing computational approaches for analysing biological processes mainly rely on simulation; but many important system properties cannot be inferred using this method. Also, simulation tells the "existence of errors, not their absence". So, it is not an efficient method to guarantee the system correctness.

LIVEBIO aims to pave the way for the next generation verification of large and complex synthetic bio-systems. The novel approach proposed in this project will permit rapid verification of complex SB systems, and provide increased assurance and trust when building new synthetic biology systems. The project will deliver an authentic and systematic certification guideline, which will allow biologists to certify their genetic parts & components and reuse them in different systems.
LIVEBIO will contribute towards biological studies (in particular, Synthetic Biology) by extending the existing portfolio of computational approaches with novel verification methods, techniques and tools. It will also contribute towards Computer Science by developing cutting-edge activities through an emerging and promising inter-disciplinary work. The impact will go beyond the project partners, and will reach national and international communities.

Planned Impact

The project outcomes will initiate a huge impact on Synthetic Biology (SB) via novel computing solutions that will allow constructing reliable, fault-free and reusable bio-systems. This will significantly reduce the costs required to develop new synthetic organisms. The project will benefit regulators and regulation bodies via a certification mechanism that will enhance the route towards standardisation and regulation compliance for Synthetic Biology.

The project will contribute to strengthening the leading role of the UK in Formal Methods and Synthetic Biology, as well as creating a wide range of novel research outputs in other relevant fields of Computer Science. The work to be carried out will lead to high impact publications on world-leading conferences and journals, attracting grants and investment from both research councils and industry, and establishing a long-term research and industry partnerships in this emerging research area. The research will have an impact on project partners and other academic beneficiaries through the generation of new knowledge, new discovery, new-engineered systems, and other exciting developments.

The knowledge, expertise and capability gained will be transferred through knowledge exchange to stimulate this impact on the UK economy. The new computational approaches to the analysis of complex bio-systems will result in novel approaches for engineering SB systems. This has clear commercial value and will contribute increasing productivity. This will open new avenues for product development and the application of SB in a wide range of industrial domains, e.g. pharmacology and bio-manufacturing.

As well as academic and economic impact, this research will also have a valuable social impact. The ultimate beneficiaries of the project are the general public. It will contribute to our ability to rapidly adopt new technologies for chronic and infectious diseases and to accelerate discovery science, e.g., in drug development and anti microbial materials. It will also help making basic SB available to people in a safe and controlled environments without working in a wet lab.

The project will also have an impact on life science researchers, PhD students and young software engineering professionals via training courses and seminars that will transfer the necessary skills and expertise. It will especially target closing the skill gap to use software engineering and high-performance computing facilities within scientific research. Our results and examples will be incorporated in several modules both across Engineering and the Life Sciences. It will conveniently help us develop new curriculums and programmes within both faculties, as well as implement joint study programmes for graduates and undergraduates.

The project will extend an interdisciplinary collaboration portfolio across the University. This will resonate with Bradford's strategic vision in the key academic themes of advanced healthcare and innovative engineering. The project also supports the University's strategic plan of making Bradford the Technology University of the North.

Publications

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