Fall 2020 - MBB 464 D100

From Genome to System (3)

Class Number: 3306

Delivery Method: In Person

Overview

  • Course Times + Location:

    We, Fr 8:30 AM – 10:20 AM
    REMOTE LEARNING, Burnaby

  • Prerequisites:

    MBB 331 and MBB 342.

Description

CALENDAR DESCRIPTION:

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.

COURSE DETAILS:

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      

LECTURE TOPICS:

-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

Grading

  • 2 Midterm Exams (2x30%) 60%
  • Paper presentation 20%
  • Assignments, participation 20%

NOTES:

  • This course can be counted towards a certificate in genomics.
  • 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

Materials

MATERIALS + SUPPLIES:

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

REQUIRED READING:

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

Department Undergraduate Notes:


  • For help with writing, learning and study strategies please contact the Student Learning Commons at
    http://learningcommons.sfu.ca/
  • Students requiring accommodations as a result of a disability, must contact the Centre for Accessible Learning (778-782-3112 or e-mail:  caladmin@sfu.ca)

Registrar Notes:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

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

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).