Introduction to Systems and Synthetic Biology

The course provides an introduction to Systems and Synthetic Biology. Participants will learn how modelling and effective experimentation intertwine to understand interactions between genetic circuits and emergent biological phenomena.

The first part of the course is dedicated to Systems Biology, which aims to elucidate the biomolecular mechanisms underlying biological processes. Student will translate biological systems into mathematical models, and learn how best to analyse these models in relation to experimental data. For this, open source computer software will be used. Particular attention will be given to the description and mathematical characterization of reaction networks and genetic circuits (notably synthetic toggle switches).

The second part of the course will introduce the principles of Synthetic Biology, including bioengineering principles, value-based innovations, safe and sustainable-by-design, and a set of experimental tools that are used to translate systems knowledge into biological engineering. Fundamental tools include automated DNA writing and reading technologies (i.e., DNA synthesis and sequencing), standardization of modular DNA parts, and the theoretical analysis and construction of biochemical and genetic interaction circuits. Students will explore the literature and debate the use of synthetic biology applications in real-world scenarios.

By combining experimental and modelling skills, the course follows the Design-Build-Test-Learn cycle, a common framework used in Synthetic Biology and engineering disciplines. First, the students will design plasmid vectors containing a genetic toggle switch and predict how the system functions using computational tools. Then, they will build these circuits by assembling standardized modular DNA parts in the lab. The circuits will be tested by measuring their output and the data will be compared against predictive model simulations to learn more about the system. Finally, students are asked to propose improved models or new experiments that could be tested to improve our understanding of toggle switch dynamics.

• Recognize the basic theoretical and applied concepts of Systems and Synthetic Biology

• Understand a biological system in terms of mathematical models

• Implement in Python a model describing a biological system

• Perform an iterative computational(dry)-laboratory(wet) experiment based on a given genetic circuit

• Employ standardized DNA assembly methods of synthetic biology to construct a genetic circuit

• Debate use of synthetic biology applications

• Reflect on the impact of synthetic biology in the near future, including its wider societal implications

• Assignment report (60%) Project where model is designed and analysed in relation to experimental data. Skills from the course will be assessed in a digital report using Jupyter Notebooks. If not passed first time, resit projects are available during resit periods to be completed.
• Written test with open questions (40%) This is a closed book paper exam covering material from each teaching week. Students are only allowed calculators to help with calculations. If not passed first time, resit exams can be taken during the resit period.

ZSS06100 Laboratory Safety Basic knowledge in mathematics, biological sciences and molecular biology laboratory techniques.

• Material (articles, tutorials, guidelines, protocols, references and suggested readings) will be made available at the Brightspace site of the course.