REI601M: Introduction to Systems Biology, Spring 2016

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.

The course activity includes reading and analyzing scientific papers, implementation of computational algorithms, working on a research project and the presentation of scientific results.

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)

Date Subject
8.1 Course introduction
12.1 / 15.1 Biochemistry basics
19.1 / 22.1 Metabolism
26.1 / 29.1 Bioinformatics - applications and algorithms
2.2 / 5.2 Reconstruction of biochemical networks
9.2 / 12.2 Optimization and Flux Balance Analysis
16.2 / 19.2 Constraint-based methods
23.2 / 26.2 Constraint-based methods
1.3 / 4.3 Constraint-based methods
8.3 / 11.3 Biotechnology
15.3 - 15.4 Project work
19.4 Project presentation

Textbook: Systems Biology: Constraint-based Reconstruction and Analysis by Bernhard O. Palsson. The book is available from The University Bookstore.

Additional reading in the form of research articles, tutorials and handouts will be provided.

Course information

Lectures: Teachers:

Evaluation

There will be 6 home assignments / case studies during the first half of the semester which account for 30% of the final grade. A student project carried out in the second half of the semester counts for 70% of the final 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/spring2016/rei601m and select "Join as Student". Click on "Join Classes" and provide your email account.