Fall 2020 - MBB 829 G100

Special Topics in Biochemistry (3)

From Genome to System

Class Number: 3060

Delivery Method: In Person


  • Course Times + Location:

    Sep 9 – Dec 8, 2020: Wed, Fri, 8:30–10:20 a.m.



Consideration of recent literature concerning selected contemporary research topics. Can be taken more than once with permission of the instructor.



Methods that enable the integration of Biochemical, Genetic and Genomic knowledge (BiGG) to reconstruct a genomic scale network that defines the metabolic physiology of an organism will be explored. Applications of these approaches in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery will be discussed.


The process of extracting biochemical content from genome annotations and literature sources to computationally catalog and interconnect the metabolic pathways available to the cell (i.e., metabolic reconstruction) is well established and has been carried out for a growing number of organisms on the genome scale. Such network reconstruction has led to the development of modeling approaches that gain a better understanding of the observable phenotypes and coordinated functions of the cell. As a result, these approaches are being used to apply and develop in silico models for biological discovery and engineering applications.  In this course we will cover conceptually some methods that enable the integration of Biochemical, Genetic and Genomic knowledge (BiGG) to reconstruct a genomic scale network that defines the metabolic physiology of an organism. We will also describe through examples computational models that integrate high-throughput data sets for prospective experimentation and validation. Finally, we will show how valuable and relevant these approaches are at making important biological predictions that can be validated experimentally. Applications in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery will be discussed through student presentations.  


- What is System Biology? 
- Network reconstruction from biological data 
- Genomic scale reconstruction of prokaryotes 
- Genomic scale reconstruction of eukaryotes 
- Biochemical networks 
- Genome metastructures 
- Biochemically, Genomically and Genetically structured database (BiGG) 
- Properties of reconstituted networks
- Phenotype potential of reconstituted networks 
- Applications in microbial evolution, genetic engineering, drug discovery, environmental science, synthetic biology and biomedicine  

Pre-requisite: An undergraduate bioinformatics course or equivalent


  • 1 Exam 30%
  • Quiz/assignments 10%
  • Individual paper presentation (20-30 minutes) 10%
  • Mini review paper in group (1 page) 10%
  • Term proposal/project paper (3 pages) 30%
  • Term proposal/project presentation (20-30 minutes) 10%


  • Lecture:  blended (synchronous lectures, recorded and available online for asynchronous viewing)  
  • Tutorial:  synchronous (attendance is not mandatory)   
  • Assessments: blended:  both synchronous and asynchronous assessments
  • Final exam: no final exam   
  • Remote invigilation of exams:  Possibly



  • Access to high-speed internet 
  • Computer with webcam
  • Free software available for download


A First Course in Systems Biology, 2nd Ed, Everhard Voit, 2017, Garland Science. E-book.
ISBN: 9780203702260

Graduate Studies Notes:

Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.

Registrar Notes:


SFU’s Academic Integrity web site http://www.sfu.ca/students/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html


Teaching at SFU in fall 2020 will be conducted primarily through remote methods. There will be in-person course components in a few exceptional cases where this is fundamental to the educational goals of the course. Such course components will be clearly identified at registration, as will course components that will be “live” (synchronous) vs. at your own pace (asynchronous). Enrollment acknowledges that remote study may entail different modes of learning, interaction with your instructor, and ways of getting feedback on your work than may be the case for in-person classes. To ensure you can access all course materials, we recommend you have access to a computer with a microphone and camera, and the internet. In some cases your instructor may use Zoom or other means requiring a camera and microphone to invigilate exams. If proctoring software will be used, this will be confirmed in the first week of class.

Students with hidden or visible disabilities who believe they may need class or exam accommodations, including in the current context of remote learning, are encouraged to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112).