REI601M: Introduction to Systems Biology, Spring 2015

Overview

Systems Biology is an interdisciplinary field at the intersection of biomedicine, engineering, and mathematics. Biochemical network reconstructions are key tools of systems biology which can be used to investigate and manipulate cellular properties using mathematical tools. This class provides an introduction to molecular systems biology by teaching i) basic principles of constraint-based modeling, ii) biochemical network reconstruction process, iii) tools to interrogate various network properties, and iv) various applications in biotechnology and biomedicine. The class also provides a short overview of biochemistry and linear algebra.

Course outcomes

Upon completing the course the student should i) have basic yet sufficient understanding of basic molecular life science in order to ii) be able to reconstruct simple biochemical networks from genomic, genetic and biochemical data, iii) be able to use constraint-based methods to analyze biochemical networks; and iv) be familiar with the main assumptions, limitations and applications of constraint-based methods in systems biology.

Syllabus (tentative)

Week Subject
1 Introduction, biology and biochemistry basics
2 Biochemistry and cell biology
3 Metabolism
4 Biochemical databases and bioinformatics tools
5 Reconstruction of biochemical networks
6 Linear algebra and optimization
7 Constraint-based methods
8 Constraint-based methods
9 Graph theoretical analysis of networks
10 Network motifs
11 - 14 Project work

The reading material will consist of research articles, tutorials and handouts. There is no designated textbook for this course.

Course information

Lectures: Teachers:

Evaluation

There will be 8 problem sets / case studies which count for 40% of the final grade. A student project carried out in weeks 11 - 14 counts for 30% and a final exam for 30%. The final exam will be closed book. The student must obtain a pass mark of 5 on the examination itself and a pass mark of 5 for the total grade. Up to 5% participation bonus is awarded to students for speaking up in class and contributing with questions and answers on Piazza.

Course web

Announcements, homework assignments and supplementary material will be posted on Piazza. Piazza also provides an online forum to ask questions relating to the course, e.g. clarification of homework problems. To sign up go to https://piazza.com/hi.is/spring2015/rei601m and select "Join as Student". Click on "Join Classes" and provide your email account.