|Teaching method||Contact hours|
|Course coordinator(s)||prof. dr. VAP Martins dos Santos|
|dr. E Saccenti|
|Lecturer(s)||prof. dr. VAP Martins dos Santos|
|dr. E Saccenti|
|L Garcia Morales|
|dr. RW Smith|
|Examiner(s)||dr. E Saccenti|
|prof. dr. VAP Martins dos Santos|
Language of instruction:
Assumed knowledge on:
Basic knowledge in biological sciences; Mathematics 2 and 3 (MAT-14903, MAT-15003) or equivalent. Basic knowledge in laboratory techniques.
SSB-30306 Molecular Systems Biology; SSB-31806 Advanced Systems Biology; SSB-31312 Toolbox in Systems and Synthetic Biology; SSB-BSc/MSc thesis in Systems and Synthetic Biology
The course provides an introduction to Systems and Synthetic biology and integrate both computational and experimental aspects of these disciplines through practicals in the computer room and in the laboratory. The course emphasizes the integrative perspective on biology of system approaches (i.e. that the whole is more than the sum of the parts) and the intertwining between modelling and effective experimentation.
The first part of the course is dedicated to Systems biology, which aims to elucidate the biomolecular mechanisms underlying biological processes by studying how higher-level properties emerge from the complex interactions among individual components of a biological system. These interactions are described in terms of mathematical models, thus it is important for life scientists to have a background in the relevant mathematical techniques, so that they can participate in the construction, analysis, and critique of available models. The course will introduce the student to fundamentals concept of chemical reaction networks, biochemical kinetics, analysis of dynamic mathematical models, metabolic networks and gene regulatory networks and their description through ordinary differential equations. Particular attention will be given to the description and mathematical characterization of gene regulation and genetics circuits (the genetic Toggle switch and the Repressilator which will then be experimentally characterized in the lab.) and oscillating systems (glycolytic oscillations).
The second part of the course will introduce the principles of synthetic biology, a set of experimental tools used to translate systems knowledge into biological engineering. Fundamental tools include automated DNA writing technologies (i.e., DNA synthesis), standardization of modular DNA parts, and the theoretical analysis and design of biochemical and genetic interaction circuits.
The course evolves around hands-on practicals in the laboratory based on a Design-Build-Test-Learn cycle commonly used in Synthetic Biology and engineering disciplines. First, the students will design plasmid vectors containing a genetic toggle switch and a repressilator. Then, they will build these circuits by assembling standardized modular DNA parts. They will test the circuits by measuring their outcome and they will relate their data to the predictions of the mathematical models introduced in the first part of the course. Finally, they will be asked to propose improved circuits and/or new genetic circuits using the knowledge they have learnt from their experiments and data.
The scripting language used during the course is Matlab: introductions and scripts will be provided and no previous Matlab experience is required.
After successful completion of this course students are expected to be able to:
- recognize the basic theoretical and applied concepts of Systems and Synthetic Biology
- describe and analyze a biological system in terms of ordinary differential equations.
- describe the properties of a dynamic biological system given its mathematical formulation
- implement in Matlab a model describing a biological system
- analyze and design iterative wet-dry lab experiments
- recognize and apply different molecular biology methods including novel assembly techniques of DNA parts.
- collect experimental data and integrate them with results from mathematical simulations and present them in a structured manner
- computer assisted practicals;
- study of relevant literature.
The final mark is based on
- written report on the computational\\experimental work (accounting for 60% of the final grade)
- exam with open questions and closed book: ½ on the theoretical/modelling part, ½ on the experimental part (accounting for 40% of the final grade)
To pass the course, the combined mark should be at least 5.5.
A suggested supporting textbook for this course is “Mathematical Modeling in Systems Biology” by Brian P. Ingalls (ISBN-13: 978-0262018883). A preprint pdf version of the book is freely available online. Additional material (articles, tutorials, guidelines, protocols, references and suggested readings) will be made available at the Brightspace site of the course.
|Compulsory for:||WUSYB||BSc Minor Systems Biology||1AF|