Synthetic and Systems Biology


This curricular unit provides basic training in the disciplines of Systems Biology and Synthetic Biology. It provides basic knowledge, competencies and skills in the mathematical modeling of biological systems and on the use of holistic models to design new biological functions. This curricular unit promotes self-learning inducing competencies to make novel discoveries, develop new methods, and establish new paradigms. Students doing this curricular are expected to be well-positioned to assume critical leadership roles in both academia and industry in topics related to the emerging disciplines of Systems Biology and Synthetic Biology.

General characterization





Responsible teacher

Rui Manuel Freitas Oliveira, Sérgio Joaquim Raposo Filipe


Weekly - 4

Total - 85

Teaching language



Frequency of the discipline of regulation of gene expression.


Mainly scientific papers.


 - D. Wilkinson. Stochastic Modeling for Systems Biology, Chapman&Hall, 2006

- Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall, 2007. ISBN: 9781584886426.

- Fu P. and Panke S. Systems Biology and Synthetic Biology, John Wiley & Sons, Inc. 2009

Teaching method

In both modules subjects are covered in theoretical lectures in standard format.
Problem-solving sessions of Module I take place in classrooms equipped with computers. Students implement models, simulate and optimize solutions of representative problems. Teams of 2 students are formed and each team will develop a project. The project consists in the implementation of an in silico cell model of their own choice based on scientific papers and databases.
In Module II classes include practical experience, in particular the analysis of bacterial strains modified with biological parts from the BioBricks Foundation catalog. Additionally, the students grouped into teams need to present an innovative idea using the available parts from the BioBricks catalog. The oral presentation of the ideia is discussed and ranked by student-peers and the teacher.

Evaluation method

Module 1 and 2 have independent grading. The final course grade is obtained by the arithmetic average of both modules. 


GRADING MODULE I – Systems Biology



A – Theoretical test

B – Practical test

C – Homework - miniproject

Final grade = 40% A+ 40% B + 20%C 

(Minimum grade for passing the module: 9,5) 


D – Theoretical exame
E – Practical exame

Final grade = 40% D + 40% E + 20%C 

(Minimum grade for passing the module: 9,5) 


GRADING MODULO 2 – Synthetic Biology


Componente teórica:

A - Theoretical midterm exam OR Final exame (Theory) – 60%. Minimal mark is 9.5.

B – Practical mid term exam – 20% (cannot be improved in the final exam)

C – Workgroup – 20%.

Minimal mark is 9.5.

Attendance of practical lectures is mandatory.

Subject matter

Module I -  Systems Biology

1 Introduction to Systems and Synthetic Biology

2 Constraints based modeling formalism

2.1 Metabolic flux analysis (MFA)

2.2.Flux balance analysis (FBA)

2.3.Metabolic control analysis (MCA)

3 Differential equations modeling formalism

3.1  Metabolic models

3.2. Synthetic gene circuits models

3.3  Properties of gene circuits models

3.4  Parameter estimation


Module II - Synthetic Biology 

1-     Introduction to Synthetic Biology 

2-     Synthetic molecules

  • Proteins 
  • Nucleic Acids 

3-     Genetic parts to program bacteria 

4-     Gene regulatory circuits  

  • collective behavior engineering

5-     Synthetic Biology and Yeast Metabolic Engineering  

6-     RNA in Synthetic Biology 

7-     Challenges in Synthetic Biology 


Programs where the course is taught: