REI601M: Introduction to Systems Biology, Spring 2018

Overview

Systems Biology is an interdisciplinary field at the intersection of biochemistry, 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 methods. This class provides an introduction to molecular systems biology by teaching i) basic principles of constraint-based modeling, ii) biochemical network reconstruction, iii) tools to interrogate various network properties, and iv) various applications in biotechnology and biomedicine. The class also provides a short overview of biochemistry, linear algebra and optimization.

The course activities 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
9.1 / 11.1 Introduction and biochemistry basics
16.1 / 18.1 Metabolism
23.1 / 25.1 Bioinformatics
30.1 / 1.2 Reconstruction of biochemical networks
6.2 / 8.2 Analysis of biochemical networks
13.2 / 15.2 Constraint-based methods
20.2 / 22.2 Constraint-based methods
27.2 / 1.3 Biotechnology
6.3 - 10.4 Project work
19.4 Project presentation

Reading material consists of research articles, tutorials and handouts. There is no required textbook for the course, however the following texts are recommended:

Systems Biology: Constraint-based Reconstruction and Analysis by Bernhard O. Palsson
Systems Biology: A Textbook by Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald and Hans Lehrach

Course information

Lectures: Teachers:

Evaluation

There will be 7 home assignments during the first half of the semester which account for 35% of the final grade. A student project carried out in the second half of the semester counts for 60% of the final grade. A short quiz will be given in the beginning of class, once every week. The quizzes count for 5% 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. To qualify for the final project, the student has to complete at least 5 of the 7 assignments and receive an average grade of 5 or higher.

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 piazza.com/hi.is/spring2018/rei601m and select "Join as Student". Click on "Join Classes" and provide your email account.