Simon Fraser University
Engaging the World

Course Outlines

Spring 2021 - MBB 342 D100

Introductory Genomics and Bioinformatics (3)

Class Number: 2563

Delivery Method: In Person

Overview

  • Course Times + Location:

    Jan 11 – Apr 16, 2021: Mon, 8:30–10:20 a.m.
    Burnaby

  • Prerequisites:

    MBB 231, BISC 202 and either MBB 243 or 3 units of CMPT or equivalent, all with a minimum grade of C. Recommended: STAT 201 (or an equivalent statistics course) or STAT 270.

Description

CALENDAR DESCRIPTION:

Major topics in genomics and bioinformatics, with integrated discussion of associated ethical/legal/social issues. An overview of laboratory and computer-based methods to study genomes, and their applications. Hands-on computer lab session providing an opportunity to use and experiment with bioinformatics software and databases utilized in genomics and bioinformatics research.

COURSE DETAILS:

Course Structure:

Approximately one week will be devoted to each of the following topics:

  1. What is Bioinformatics? What is Genomics? An overview and history
  2. Obtaining the data: Genome sequencing, genome assembly
  3. Organizing the data: Gene/genome databases, browsers and searching
  4. Sequence alignment and sequence similarity search
  5. Genome assembly and short read mapping
  6. Human genome variation – SNP, copy number and structural
  7. Transcriptomics/RNA sequencing, chromatin IP and promoter analysis
  8. Multiple sequence alignment, intro to evolutionary analysis
  9. Orthologs, paralogs/gene families, phylogenetic analysis
  10. Protein, network-based analysis and Systems Biology
  11. Microbial genomics and metagenomics of environmental/human microbiomes
  12. Human genomics and personalized medicine
  13. Plant and animal genomics in agriculture and aquaculture

Grading

  • Lab assignments 40%
  • Two non-cumulative written exams during class time (synchronous) 40%
  • Lab assignment/project 20%

NOTES:

  • Lectures:  blended (synchronous lectures, attendance is not mandatory; recorded and available
    online for asynchronous viewing)
  • Labs:  synchronous (students attend scheduled labs remotely)
  • Assessments:  blended; both synchronous (mandatory attendance) and asynchronous assessments
  • No final exam
  • Remote invigilation:  Possibly

Materials

MATERIALS + SUPPLIES:

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

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 SPRING 2021

Teaching at SFU in spring 2021 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).