Molecular Systems Biology
1
2020-2021
02038812
Computational Biology
Portuguese
Face-to-face
SEMESTRIAL
6.0
Compulsory
2nd Cycle Studies - Mestrado
Recommended Prerequisites
Linear algebra (matrices, determinants, eigenvalues and eigenvectors, solution of linear systems)
Differential and integral calculus (systems of ordinary differential equations)
Numerical methods for integrating differential equations
Basic notions of molecular and cellular biology
Reading and interpretation of scientific texts in English.
Teaching Methods
Oral presentation using audiovisual and computational resources. Practical group work (mini-projects) to develop modeling skills and apply them to research problems. The theoretical-practical classes will be devoted to the execution of the mini-projects, discussion of their advancement with colleagues and teacher, and the discussion of relevant primary literature.
Learning Outcomes
Upon completion of this course unit the student should be able to:
Construct and analyze constraint-based models of metabolism.
Model the dynamics of biochemical circuits using deterministic models.
Use quasi-equilibrium, quasi-steady-state and functional approximations to simplify models.
Use sensitivity and stability analysis to investigate the systemic behavior of biochemical networks.
Understand key concepts and conventions of Metabolic Control Analysis and Biochemical Systems Theory.
Estimate parameters from biological time series.
Use the main publicly available data resources for modeling and model repositories.
Understand key concepts in Systems Biology, such as robustness, ultrasensitivity, feedback/feedforward regulation, network motifs.
Recognize the main regulatory motifs of biochemical networks and understand how their design relates to function.
Work Placement(s)
NoSyllabus
The fundamental scales of Biology
Generic properties of biochemical networks
Introduction to chemical kinetics, including enzyme kinetics
Constraints and optimality of biochemical systems
Constraints-based modeling of metabolism
Deterministic modeling of the dynamics of biochemical networks
Setting up models
Handling conservation relationships and compartmentalization
Numerical integration of systems of ordinary differential equations
Data sources for modeling and model repositories
Quasi-equilibrium and quasi-steady-state approximations
Functional approximations
Local stability analysis
Brief introduction to bifurcation analysis
Sensitivity analysis
Parameter estimation from biological time series.
Elements of control theory
Introduction to Metabolic Control Analysis and Biochemical Systems Theory
Properties of widespread regulatory motifs in biological networks.
Head Lecturer(s)
Armindo José Alves da Silva Salvador
Assessment Methods
Assessment
Exam: 50.0%
Research work: 50.0%
Bibliography
Alon, U. (2019) "An introduction to Systems Biology", 2nd edition, Chapman & Hall/CRC
Voit, E. O. (2018) "A First Course in Systems Biology", 2nd edition, Garland Science.