Molecular Systems Biology

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)

No

Syllabus

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
Research work: 50.0%
Exam: 50.0%

Bibliography

Alon, U. (2019) "An introduction to Systems Biology", 2^nd edition, Chapman & Hall/CRC

Voit, E. O. (2018) "A First Course in Systems Biology", 2^nd edition, Garland Science.