Simon Fraser University
Engaging the World

Course Outlines

Fall 2021 - MBB 243 D100

Data Analysis for Molecular Biology and Biochemistry (3)

Class Number: 4281

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 8 – Dec 7, 2021: Tue, 8:30–10:20 a.m.
    Burnaby

  • Exam Times + Location:

    Dec 15, 2021
    Wed, 7:00–10:00 p.m.
    Burnaby

  • Prerequisites:

    MBB 222 and MATH 152 or MATH 155. STAT 201 (or an equivalent statistics course) or STAT 270 is recommended.

Description

CALENDAR DESCRIPTION:

Introductory data analysis focusing on molecular biology data sets and examples and including basic programming skills using Python and basic statistics skills using R.

COURSE DETAILS:

The purpose of this introductory data analysis course is to teach students in molecular biology or any students who will analyze molecular data, basic knowledge of molecular biology data types, data analysis methods including basic programming skills using Python, and basic statistics skills using R.

Lectures

Lecture 1 Molecular biology data and data analysis.
Lecture 2 Molecular sequences: features & composition.
Lecture 3 Gene splicing and GFF data format.
Lecture 4 Sequencing analysis using Biopython.
Lecture 5 Quantitative DNA analysis using Python conditional test.
Lecture 6 Searching for restriction sites in DNA sequences.
(Midterm exam)
Lecture 7 Searching for sequence features in protein sequences.
Lecture 8 Genetic code and DNA translation.
Lecture 9 Quantitative analysis of genes using R.
Lecture 10 Analyzing genomics big data using R data frame.
Lecture 11 Genome annotation using R data frame and R graphics.
Lecture 12 Genome analysis using Bioconductor.
(Final exam)

Labs

Lab 1Learning Python: printing and manipulating sequences.
Lab 2Reading and writing sequence files.
Lab 3Lists, loops, reading large sequence files.
Lab 4Writing our own functions for processing sequences.
Lab 5Quantitative DNA analysis using Python conditional test.
Lab 6Using regular expressions to search for sequence features in DNA sequences.
Lab 7Using regular expressions to search for sequence features in protein sequences.
Lab 8Translating DNA sequences using Python dictionaries.
Lab 9Learning R: molecular data analysis and presentation.
Lab 10Working with genome-scale sequences.
Lab 11Using R data frames and R graphics
Lab 12Technical review

Grading

  • In class lab tasks: In each lab, there is a list of tasks that should be accomplished in class. Results are submitted by the end of each lab. 20%
  • Lab assignments: Short assignments will be handed out in lab sessions and will be due at the start of your lab one week later, unless indicated otherwise. There is a 10% per day late penalty for assignments received after the due date time. 35%
  • Midterm and final exams - a mixture of multiple choice, short answer and written questions. (10% for midterm exam and 25% for final exam) 35%
  • Participation 10%

NOTES:

Students with credit for CMPT 102, 120, 125, 126, 128 or 130 may not take this course for further credit.
Lectures:  in person
Labs:  in person
Assessments:  in person
Final exam: Yes

Materials

REQUIRED READING:

Python for Biologists.  Martin Jones.  2013. CreateSpace Independent Publishing Platform.
ISBN: 978-1492346135

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 2021

Teaching at SFU in fall 2021 will involve primarily in-person instruction, with approximately 70 to 80 per cent of classes in person/on campus, with safety plans in place.  Whether your course will be in-person or through remote methods will be clearly identified in the schedule of classes.  You will also know at enrollment whether remote course components will be “live” (synchronous) or at your own pace (asynchronous).

Enrolling in a course acknowledges that you are able to attend in whatever format is required.  You should not enroll in a course that is in-person if you are not able to return to campus, and should be aware 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.

Students with hidden or visible disabilities who may need class or exam accommodations, including in the context of remote learning, are advised to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112) as early as possible in order to prepare for the fall 2021 term.